The mufflers I have are a straight-through design. One has a center inlet/offset outlet, so it does have a slight "Z" path to it. Keeping with this design won't affect the tune or performance at all.
Factory piping, at least on my GMT900 is 2.75". You could do Y to split your current pipe into two 2.25" to go into the mufflers placed side-by side, then Y them back together afterward and continue out as a single pipe. But, I think that'd hurt the flow and overcomplicate things. I'm a fan of the Magnaflow clones from AP Exhaust (Xlerator series) because they seem to be identical in function and quality to the Magnaflow, but are half the price or cheaper. But, I can't say if the stainless is a lower grade or not and might not hold up as well in salt cuz that's not an issue here.
Here's the 40" of muffler crammed under mine:
https://www.tahoeyukonforum.com/threads/growing-up-doesnt-have-to-suck.93510/post-1485217
I forgot about the cutout. If it weren't for that, I could fit another ~10" or so of muffler.