For the most part, you can read them in any order you like until around the late 40s (read #20-#22 in that order though because that's the David Trilogy). But I would recommend reading them in chronological order. That puts Megamorphs #1 between #7 and #8, MM2 between #18 and #19, MM3 between #29 and #30, and MM4 between #40 and #41.
As for the Chronicles: The Andalite Chronicles can pretty much be read whenever, however, I'd place it either before #1 or after #54. The Hork-Bajir Chronicles should be read between #22 and #23 and Visser should be read right after #35. The Ellimist Chronicles should not be read until you've completed the series.
If you want to waste your time with read the Alternamorphs, they can pretty much be read whenever.