Almost all of your questions can be answered by taking a look at the following links. As there are several MegaSquirt code forks, there are a couple different manuals out there.
MegaSquirt manuals at MSExtra.com – This covers the MS1/Extra code, MS2/Extra code, and MS3. Subjects covered include assembly, firmware, and tuning. These are the most popular code options, with the most features and easiest usability. Recommended for most installations.
MSExtra.com Forums – Official support forum for MS1/Extra, MS2/Extra, MS3, and MicroSquirt transmission control code. Covers all board variants, including MicroSquirt. This is the most active of the official MegaSquirt support forums, and often the one you’ll get an answer fastest.
MS3-Pro – Documentation for the MS3-Pro system.
MSPNP.com – Includes installation, documentation, and base maps for the MSPNP line of plug and play systems. Also see the manuals at MSExtra.com, above.
MegaSquirt EFI Forums – Support forum for Bowling & Grippo code for MS1 and MS2. Extra code variants are not covered; see the MSExtra.com forum for support if you are running one of these versions.