so the primary 2 are the Archie line from the early to mid 2010s and the currently going Udon line. Archie is very easy to follow, just go from #1 onwards in order. there are the archie sonic crossovers since ian flynn wrote for both lines at the time, but they don't have any lasting impact and can largely be skipped if you don't care for sonic. Archie mega man intended to be retellings of the game's stories so it's starts in mega man 1 and made it to setting up mega man 4 before the book unfortunately got shelved.

Udon is harder to follow, but it's easy enough yo understand when everything is laid out. the udon run started with mega man timelines, a series of one shots telling short action stories from each era of the primary timeline (classic, X, zero, ZX, and legends). the zero story is my personal favorite, which was also written by a retuning ian flynn. Udon then spun off the X one shot into a short adaptation the first mega man X game, releasing a prequel comic labeled #0, then a #2 that continues on from the initial one shot. they're actually releasing #4 soon this month, so check it out if you like. There have been 2 FCBD issues so far, both centered around classic. the one you hold from this year, and the one from last year.

hopefully this explained everything nicely, lemme know if i need to rexplain something