When I hit 50,000 in a couple months, I want to clean the whole system out. Can I blow air the supply line to drain the whole system, or is there a better way?

I have blown air into the mainline pressure tap and usually get another5 quarts out.

I've flushed my complete system twice, the "hoot" way.

Drain pan, replace spin-on filter. Fill pan with new fluid.
(Stock pan capacity is 7.4 qts. System capacity is 12.7 qts.)
Now remove the tranny cooler return line from passenger side of tranny by removing spring clip, and then pull out line from tranny. Install some soft tubing over remove cooler line, and direct this to a container you can measure with, (a milk jug could work, but something larger would work better. Start engine, (a helper works good), and the tranny will pump fluid out into your container, at a rate of maybe 2 gal/min. When you pump out about one gallon, stop engine, and add another gallon of new ATF to tranny.
Be certain NOT to pump system empty!
Theorietically you now removed 7.4 qts, (tranny pan capacity) plus 4 more qts, from a 12.7 qts system. Personally, I would pump out one more gallon of fluid, to better assure you flushed most of the system. Then add 4 more qts which should get you filled near recommend level. If you have the deep pan, this usually adds about 3 qts to the system capacity.
Remove drain hose, reinstall cooler line in tranny and reattach spring clip. Ensure tubing is securely attached to tranny.
The Helms Manual, or maybe Allison, recommends not reusing this spring clip, but it sounds like most people reuse them, as I have. I briefly searched to find extra spring clips, (Dealers), but couldn't even find a part number. I haven't been at a Allison Dealer, who may also have them.
Warm tranny fluid to 160 - 200 Deg F to accurately verify fluid level, (and be certain to not over-fill), when fluid is at this temp.
Info found at hoot's personal info at link below.
http://www.getdieselpower.com/my01dmax_files/allison/allisonflush.htm