Hi Jenna, I love when I hear a farm owner moving toward a true compost program. With a facility your size is a wise move.
My best advice is to visit the best resource I can offer; Peter Moon at O2 Compost. Here's the link to the website: http://www.o2compost.com/
Peter will recommend using pellets primarily, however (at the risk of sounding self serving here) he has also tested our mini flake shaving and has found it equally effective in producing a high quality compost.
Basically, the smaller the particle the faster it decomposes. With the smaller particle, your manure pile becomes a lesser percentage of wood ( carbon) mixed with the manure and urine. O2 Compost is definitely the "expert" here so take a look at his very informational site.
Let me know if you have further questions. Thanks so much.