This is something I've had a lot of trouble with, also. Your best bet is to study, man. Look how other composers do it. I been analysing a few of Shosta's symphonies which has helped - although at the same time making me feel really insecure about my own large scale works :-P
The only other thing I could advise is to try and imagine the flow of music from one theme to the next in a non-musical sense (whether it is in a programmatic sense, or a transition of "feeling". I'm a chromothesete, so I see a change of colour) and then try and emulate that within your music. Might not work, but I find when I'm stuck, re-imagining an idea can help as well.
