So, I've got more questions about MS and I can't find my old thread, so here I am.
Questions (all are for a fuel only setup):
When installing/tuning MS, how are the fuel maps generated? Are they plotted point by point? Is there a baseline curve that you modify?
What inputs go into the making of a fuel map? Just fuel and air?
Is MS a "learning" system? Will it adapt to one's driving habits?
Thanks for any answers, I'm sure they will generate more questions. 
This is all covered in the MS manual on http://MegaSquirt.info you really should go and read it.
If you use TunerStudio then you can plot a "basic" fuel table based on the engine parameters. It won't be correct, but it should be close enough to get you up and idling with some adjustments and then you can adjust the overall fuel map or a group of cells to get it closer so you can slowly drive the car and fine tune the individual cells based on the oxygen sensor feedback.
Depending on the version of Megasquirt you're using, you may get an 8x8 table or a 12x12 table to work with. The scale for the table is typically a MAP or TPS value on the vertical axis and RPM on the horizontal. When you enter the parameters to build the default table you enter a max RPM range and that is the last table used on the bottom row at the very right.
However, these are adjustable by simply clicking on the labels and entering a different number. This way you can provide more or less granularity to certain areas of the table, especially helpful for cars that are boosted or run run ITBs, etc. as you want to tune the fuel for the areas where you drive the most (cruising, etc) and where you see more changes in fuel requirements. Higher RPM and decel areas don't need as much fuel control.
The inputs needed are either the MAP (for Map or engine vacuum based fueling, the default) or the TPS (for Alpha-N, used in ITB and low vacuum signal solutions) and RPM. If you have a Wideband oxygen sensor (and you should) then you can use that to tune the fuel table and then allow the sensor to make fine adjustments once you get it close.
MS itself will only adjust based around the parameters you provide it. TunerStudio which is a tuning software available for MegaSquirt has a mode for auto tuning the fuel table, but you need you need to have it running on a computer while you drive the car. After the tuning is close, the oxygen sensor can be used to make small adjustments based on the parameters you set (when it becomes active, how much adjustment it can provide, etc.)
If you don't have TunerStudio then you can log runs in the car with a computer and adjust the fuel table based on the logged data using LogViewer from EFIAnalytics, which also has the ability to auto tune the fuel table by reading the log file.
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