When should I take Xifaxan 550mg tablets?

You should probably take the capsules between 5 and 8 hours apart.
Why? The package insert says that, in IBS patients who take a 550mg tablet 3x a day, it takes about an hour to reach peak plasma concentration, and it has a half life of about 6 hours. That suggests that you should wait at least 5 or 6 hours between pills, which roughly corresponds to a breakfast-lunch-dinner schedule.
However, you do not need to take Xifaxan with food. If you take it every eight hours, regardless of your meal schedule, that will probably result in fewer changes in plasma concentration.

If your Dr. did not specify if it is to be taken with each meal (breakfast-lunch-dinner) or every 8 hours (8am-4pm-12am).

I suggest you contact your Dr. and clarify this situation.

https://www.drugs.com/xifaxan.html