I was taking cholestryamine for bile salt diarrhea after having my gall bladder removed. My experience may or may not be relevant to yours.
I was taking two doses per day, but I don’t recall at what times. It worked, but it was inconvenient to use the powder and I found it somewhat distasteful. I asked my physician about taking a pill instead, and was prescribed colestipol hydrochloride tablets. That works as well, I suspect because it specifically addresses bile salts. I find it easier to deal with than the cholestryamine powder.
“Not going so well” doesn’t give me a clue as to what problem(s) you’re experiencing.
I don’t know if the timing is significant, other than to space the doses out fairly evenly. It may be that two a day isn’t quite enough for your particular condition. My thought is to go back to three a day for a long enough period to feel secure in that, then perhaps try to reduce slowly. You could cut out the third dose every third day for a while, then every other day, etc. I think you’ll have to experiment to get it just right for you.
As a tangent: I never wound up needing it, but was given some “just in case” when a gallbladder attack caused cholestasis and intolerable itching. I was cautioned to take it well before or well after other meds because it impedes absorption of the other medications.
That, in my mind, would be a reason to try to reduce use of the stuff if possible (if the OP is on other medications).