I have two chippers (one petrol, one electrical both with max. diameter of 5 cm) but unfortunately both are too small for chipping larger branches not to mention trunks.
This spring I've decided to remove about 50 apple trees and since I didn't want just to trow whole trees away I did this:
- removed limbs/branches and moved logs away
- cut larger branches into smaller parts (trying to have them as strait as possible)
stacked branches in few piles so that thicker part of branches are aligned in same direction (towards the chipper) for easier feeding into machine (like in my superb drawing :D )
\ | /
| <- (piles of branches)
Most chippers have some kind of funnel shaped opening/feeder so you can't really put branches in reverse position. Once the chipper grabs one end of branch and starts grinding, it will continue to pull in the rest of it.
If chipper is manually loaded, having branches aligned in same direction will shorten amount of time (and stress if branches are tangled).
Anyway, IMO it all depends on size and type of chipper. With really big machine it doesn't really matter what goes in and in what direction.