Great news, let the battle begin. To answer your question....I would stop all other probiotics during your FTs. If you still have D, I think you could keep S. Boulardii going though. Once the D stops, you could stop that to and just finish up the FT protocol.
I recommend you guys youtube, "Dr. Lawrence Brandt, fecal transplant, Ulcerative Colitis". He is the US version of Borody, and the one that helped guide my son via emails through his early FT days. Anyway, he very candidly and confidently talks about his views on FT and the future regarding its impact on IBD. I think there is a 3 part interview. He is reported to be the first to do the FT via colonoscopy. He supports the infection theory, but acknowledges an autoimmune reaction and combination of the two in IBD.
Hang in there Bananagirl, keep at it and keep posting. We ALL want to see you be successful.