I am going to try a week course of Flagyl that my doctor prescribed me after I brought up trichomoniasis as a possibility for my condition. I know antiboitics are hard on the body and I am wondering what I should do before/during/and after to help my body in dealing with the ABs, and repair any damage that they may do.

Flagyl acts as an antibiotic (towards some bacteria) as well as an antiparisitic. Therefore, when you are done, load up on probiotics for awhile.