I'm not sure that I understand the process that you're using. It sounds fairly complex.

Basin filling conceptually works by setting "water" to a high level on the whole surface and then draining it away, letting it pool into the low spots of the surface. When all of the water drains away to the lowest level that it can, the software "freezes" it all into land. Wilbur treats the "lowest level" as either the lowest point on the edge of the map or any point below zero on the surface. If you paint one pixel at the low spot of a basin to a value below zero such as -1, then the "water" will all drain away into that sump, preventing the basin from being filled. So... if you want to keep a basin through a basin fill operation, put a drain (at least one pixel below zero) where you want the basin to stay. You'll probably want to get rid of that drain before doing other operations such as precipiton erosion, though, because precipiton erosion will start pulling in altitude to fill the drain.

One way to make sure that you have drains is to use a selection with little spots for the drains that you always want to keep. Before any basin fill, load the selection, set the surface to -1 (setting only the selected spots to -1), select all (or load some other selection for basin fill), fill basins, then eliminate the drains by loading the drain selection and using Filter>>Morphological>>Median (or any of the morphological filters because they will select the maximum, minimum, or most common value in the local neighborhood).

Being able to pan around the surface while a modal dialog is up would take a good deal of work because of how the system message loop operates. It's not something that's likely to happen any time soon, unfortunately.