This idea was pioneered by Dave York. He wrote an article for the old Slant Six News. Here is what he did:
The pictures weren't really clear, and I wanted to try this myself and put the throttle bores in the factory location so I tried this experiment myself.
I used many power tools for this project: a sawzall, a 4 inch grinder, a drill press, a tap and die set, a pair of vise grips, and a dremel tool. The grinder and a drill are the only really necessary tools, but a dremel and a sawzall REALLY make life easier.
First you cut the carb mounting pad off and grind the manifold roughly flat:
Then you use an old two barrel carb base gasket to trace the outline of the throttle bores where you want them, and drill a series of small holes on the perimeter of the bores:

Fortunately cast iron is brittle and you can give the intake a good whack with a hammer and the drilled out portion will break right off.
At this point in the project a problem became very apparent to me. The Super Six intake manifold has a slightly different shape to the "box" the carb sits on. This minor design change allowed for the wider bolt pattern of the two barrel carb. Also on the two barrel intake the outboard boss is gone for the one barrel carb so the area for the throttle bore is much wider. On the one barrel intake the is not enough space between the outboard one barrel carb bolt boss and the boss for the inboard intake to exhaust manifold bolt boss to mount a two barrel carb. The picture below shows the exhaust bolt boss protruding into the new two barrel throttle bore:
This a picture down into the intake showing that the boss for the intake to exhaust manifold bolt is to big to be ground down or drilled out:

I will address how I compensated for this later.
I used a Dremel tool to grind the intake to as close to the two barrel outline as possible:

This helps a little with the boss blocking the bore, but not much.
This is where my method differs somewhat from Dave York's. Instead of buying a pre-fab aluminium carb adapter and bolting/JB Welding it to the intake, I fabricated my own carb mounting pad out of flat steel I bought at my local home improvement store. This allowed me to compensate for the boss sticking into the bore by making the mounting pad hole oversize and cheating it towards the driver's side of the intake. It is not an elegant or even pretty solution, and it doesn't completely eliminate the blockage by the boss, but it helps and is much better than not doing it. (Note 1- See Below)
The next step is to carefully coat the mating surface on the intake manifold with JB Weld or some other similar epoxy:

This is an important step since this acts both as a gasket between the carb mounting pad/flange/adapter and it is how your carb mounting device is secured to the intake (Note 2- see below)
Here is a picture of my end result next to my cracked factory aluminium Super Six (if you look close you can see the crack):
Thats it! This whole project too me three nights working with power tools, so you could probably get it done in an ambitious weekend with or without power tools. Dave York says he cut his carb mounting pad off with a hacksaw. Well, he must have arms and a back like a bodybuilder since I had a hard time doing it with my sawzall. I highly recommend using power tools for this project.
Dave York's method was actually easier in two respects, both due to the throttle bore orientation. Making the throttle bores run parallel to the engine give you more room to drill the new bores and you aren't going to run into any bolt bosses. This also allows you to use the aftermarket carb adapter like Mr. York did rather than fabricate your own like I did. Unfortunately this means people with automatics are going to have to fabricate some other sort of kickdown linkage and you won't be able to use the factory choke provisions.
If you know you are never going to use a Holley 2280 or Carter BBD carb, you CAN use the small to large two barrel carb adapter made by Mr. Gasket to mount the carb in the same direction as the factory did without building your own carb mount from scratch. I wanted to be able to run both stock carbs as well as mount aftermarket adapters so I made my own carb mounting plate and tapped the holes so I can remove the studs later.
At the end of the day I think it is much simpler and more practical to just go buy an aftermarket or factory Super Six intake. The only advantage I see to doing this project the way I did it is if you ae using some really weird carb or throttle body and can't find an adapter for it or you don't have clearance to run adapters or just want to have the carb or throttle body bolt right to the intake.
I only recommend doing this project if you absolutely cannot find a factory two barrel piece or do not have the money for a factory or aftermarket manifold. Seing as how used manifolds can be bought for $30-150 depending, I really think it is better to just buy one pre-made. However, if you like to tinker with stuff and want to create your own custom intake, then this method should work for you. Its ugly, but it will work.
So there you have it. It IS possible to turn a one barrel intake into a two barrel, but it is really a paint in the butt. My intake is ugly because I was building it mostly to see if it could be done. Someone with better metalworking skills and more desire to build a nicer looking manifold could do a much better job. This manifold also has numerous problem which make it not a very good choice for racing applications (but hey, if you have the money to go racing just buy a real manifold!).
Note 1- I used three inch wide steel that was either 1/8 or 3/16 thick (I can't remember) I cut two plates roughly four inches long, welded them together, and drilled out the throttle bore like I did on the intake manifold and drilled and tapped the holes for the carb studs. Steel is not easy to drill and tap, nor is it easy to drill a throttle bore into. I was using a drill press and I still broke several bits, including one instance where the bit froze in the piece and the piece spun madly before breaking the bit and flying across the room. Fortunately I was uninjured and nothing was broken. Point is, be careful. In making this plate I had to do a lot of grinding work to clear the intake to exhaust manifold nut and bolts. Keep that in mind if you decide to try this. Making my own mounting plate did allow me to cheat the throttle bore to the driver's side slightly. This combined with grinding the bolt boss down as much as I could reach really helped to eliminate much of the boss' interference with the throttle bore.
Note 2- I am also going to weld my pad to the intake as soon as the JB Weld sets up. I don't want to leave any possibility of a vacuum leak. Bear this in mind if you make your own carb mounting pad- you either need to have absolute faith in JB Weld or have access to a welder.