What I do is create the sequence on the simulator, then open the .esq file in a text editor. Pretty simple XML format, so it ain't hard to change things without mucking anything up too badly. I know that's perhaps not as smooth a user interface as one might like, but it gets me moving forward. I've even done the same with .esl schedule files.
My approach is connect the camera and then create a basic set of simple capture sequences: it only contains gain, offset, filter, exposure time and number of frames, for example 1h total exposure using 600s subs and filter Lum (6 frames). They only have one line on each
Latter, I can create session files on the scheduler combining the target information with this capture sequences and using the repeating N-times on scheduler to increase the exposure in 1h blocks.
Sorry I didn't see your question before. More often than anything else, I change the folder the subs are saved to. And I seem to frequently find myself messing with the exact mix of exposure time and # of subs, though the latter is easy to control per rbarberac's suggestion. So if I created a sheaf of sequences for single filter-exposure-gain combos, I guess I could combine 'em in the scheduler. Interleaving filters would make it more complicated, of course.