On the older non WG Banks setup both auto & manual run up the driver's side. The difference is in the pedistal/top bracket. The manual bellhousing goes straight back about 1" then drops down whereas the auto is straight down. The bracket includes the top turn of the up-pipe, and the up-pipe runs right up on the bellhousing, so on the manual the casting has to be extended aft further to acommindate the pipe having to be further aft to clear. If you try to use an auto bracket on a manual the pipe can't meet up with the casting flange.
The manual pipe may be slightly smaller diameter as well due to the reduced clearance, but I'm not sure. Don't think the small different in casting would require any other significant changes, so my suspicion is that either up-pipe will probably fit.
No reason you couldn't use a manual setup on an auto trans.
Now, the WG setup is completely different with both pipes going up the passenger side. AFAIK there is no difference between auto & manaul, but I'm not sure.