This is how I littered box trained my bun.. He poo's and pees in his "litter pan" same place where I put his hay.. I also havea hay bin for him that he is not all that "keen" on, so I change his litter pan every other day.. When he is out in his "hutch" which is 2 X5 ft,he has no litter pan but "goes" only, in one corner (same w/his litter pan).. Assuming buns will have specific requirements for the "bathroom" habits I've not found a problem w/feeding hay to him in his "potty" box.. But you need to find what works for your bun..
EDIT: Also Baxter! my bun seems to have one of those tummies that can take anything, so if your bun is "sensitive" I would not recommend this..
You need to figure out what dietary issues you may be dealing with - to avoid the GI Statis problem..
I just got REALLY lucky and do not want to suggest that this is normal.. Most buns from what I see, need to go "slow" and "clean" w/the foods they digest. Do not introduce new foods to often and make sure "everything" is clean..