I try to make the best of the good days and manage the bad days. When I don't feel bloated, or have bad D, or pain, I get out and do the things I enjoy doing. With work, the days I feel good I try to make as much progress as possible on my projects so that when I hit that rough patch I have the flexibility to take time to rest/stay by the toilet etc.
The lack of motivation that you mention is tough. This complicates what I described above...you may be feeling ok physically, but mentally you are wiped out, depressed, apathetic, or some combination thereof. What I do on these days is manage it the same way as a bad physical day. I don't beat myself up that I feel down or unmotivated, I just find a way to ride it out and minimize the damage/impact on my life. I think we tend to have guilt that we feel mentally or emotionally down/out of it - especially when we feel decent physically. But, we have to accept that these diseases can wear us out mentally and emotionally as well. There is nothing wrong with that, its a normal part of having a chronic disease.
Sometimes I think of it this way...if life is a journey, then there will be some days where we travel many miles, some days we may only walk a hundred yards, and there may be some days where we just have the strength (physical, mental, or emotional) to only make a single step. Understanding that, and accepting those days which are a "single step day" helps me keep perspective. On those days I try to identify something that I will do that day, and do it. It may be as small as, "get out of bed and brush my teeth", but I am content to do that one thing and then get the necessary rest etc.
Hope I wasn't rambling, just sharing my perspective on it.