If you can't find acidopholus at a health store, a little plain yogurt with each meal will also help a bit. It has to be an active culture yogurt and have no added sugar or artifical sweeteners in it. It's not a strong probiotic but will help some. This is something that you can easily give a few hours after you give the antibiotic (but don't give them together).
As for length of treatment--we've had so much better luck going long than just treating for 3 weeks. Our one and only anaplasmosis relapse was on hubby, who only took the doxy for three weeks. The dogs have all had it for 4 weeks or longer (typically 6 weeks if they can tolerate it that long) and none have had any relapses.
Also, after she is asymptomatic and done with the antibiotics, some of those followup tests MaxaLisa mentioned are a good idea. Although your girl didn't test positive the first time, that doesn't necessarily mean she was just at the onset of the disease. The tests miss up to 30% of the cases and sometimes you never get a positive at all. So at least a followup CBC is in order to make sure platelets and RBCs are back to normal. And since these disease can be so hard on the organs, if you can afford it, a full blood panel checking for organ function might also be a good idea.
"We are--each of us--dying; it's how we live in the meantime that makes the difference."
"It's not what you gather, but what you scatter that tells what kind of life you have lived!"
"Be kinder than necessary, for everyone you meet is fighting some kind of battle."