So you know the problem is that she's upset about you being away and telling you the only way she can(by pooping in the wrong place) please try not to be too angry with her she's only trying to tell you that she's upset when you are gone.
I'm not sure how to solve this one. You could limit her space on days you know you're going to be away that night but I imagine it would mean putting her in one room with her litter box and food when you leave for work and have her be there until the following night when you get home?
If it were me I think I would only stay over at my boyfriend's when I could bring her with me. Does he hate your place? Is there a reason he doesn't come stay at your place during the week? Is your place too far from his work? The other solution is to just move in with each other and be done with it