This thread's goal is to familarize the reader with setting up their megasquirt and beginning of tuning to warm-up and advanced tuning. most of the information can be found in the megamanual and will probably be a reiteration. However, I find that now that I have gone through the process I can simplify and clarify. I'm currently enrolled in a Techincal Writing class, so this is also some decent practice. The reader must be familiar with terms and have at least breezed through the megamanual; besides a basic understanding of mechanics and computers. This will not cover the mechanical setup of your fuel injection you can search how I did mine under "how to TBI" or research the more work intensive part of this project, this will solely cover what I have done and the phases should be coverd in thread posts and will include the steps.
Connecting Laptop
Communications -> Settings
Under Port select which comm you believe you have most likely plugged your USB into, than select test. If failed select another port; other symptoms include setting the serial data rate at 9600 and 75msec time interval.
Setting TPS
Tools -> Calibrate TPS
Instructions are pretty straight forward though an important step.
Setting Constants
Setting up constants will be where you will start at, this can be found under basic settings. Insert values on the main page first according to you set-up, it should look similar to the picture below. Next, click on the Required Fuel and insert the size of your engine and injector flow.

Note: The PWM setting are set on either high or low impendance injectors. This setting is based on current with high often being greater than 10ohms and low less than 4ohms.For high impendance insert values 25.4 msec at 100%, and for low insert 1 at 30%. For Opening Time and Battery Correction I suggest copying the values in the picture above.

Creating a VE table
This next step is to create your VE table, this is what will control your fuel and will be the area of study over the course of tuning your car. Though powerful can be frustrating so prepare to fight and save often. At this point I would suggest acquiring a copy of MegaLogViewer as it will be money well spent as well as a invaluable tool in tuning. More to come later.
Open the VE table under Basic Settings -> Fuel VE Table 1. On doing so click on Tools -> VE Specific -> Generate Table. This should give you a very rough map, but one none the less. For a mild street build with moderatly large injectors I would suggest something along the image below, otherwise refer to dyno sheet or personal guess.

Note: In contrast to a finished version of my personal fuel map this will always give you a safe ,rich map. This is an ok starting place, but be weary.

Cold Start Enrichments
This is set after a basic fuel map is set, and though you are probably clear to start your engine assuming that your ignition is still controlled by mechnical distrubutor, lets continue to hone in on the rest of the settings.
Cranking Pulse Width
Let's not complicate this anymore than we need to, this is the fuel being delievered while the engine is cranking. This is measured in milliseconds of the injectors being opened to let the fuel come in. The beginning values will be constant .1. I suggest working somewhere around 20 for the top value (-40) and evenly distruputing something like what I have. If youe engine is taking a long time to start, stop cranking, and allow your O2 sensor to warm-up telling you what the AFR is. Richen (often) or lean accordingly, flooding is still possible.

Afterstart Enrichment
This is simply the amount of fuel that is delievered to the engine after the cranking is complete and the engine has started. This setting will often control the fuel for about 10-15 seconds after start. The diagnoses is to richen fuel if the engine stumbles and dies, making sure to read your O2 sensor. The O2 sensor will be your primary source in diagnosing rich/lean settings which can assist in honing in on the correct AFR. Be patient enough to make sure you let the sensor "warm-up" or you will always read rich.

Once again I would start something around 25 and work down the table accordingly.

Warp-up Wizard
This is one of the simpler parts to work with. The tables before were all values inserted, this is still the same but has dec/inc buttons which help. The warm-up wizard is only used once the engine has started and has ran for about ten seconds. If you note that the colder temps increase the fuel by somewhere around 150% I would advise starting at this and working your way down proportionly. This is normal, in fact could be enrichened even more if wanted. After the engine has warm-up to at least 160deg should you now be looking at the VE table. However, if it is too much fuel and you are at this stage you can consider adjusting the VE table slightly assuming it is the table that is generated not a worked on map.

After and only after you've filled in some values for the crank/warm-up should you start to tune the VE map we generated above. Please don't add any comments to this thread as it is a work in progress. If you want to comment write a message(encouragement, appreciation, waste of time) or start a new thread. Hopefully this will be a better starting place for some. Wes