To make optimal use of the software, you must keep in mind that layers drawn first will appear the furthest back in an image. Eg. If you mask siding then mask trim, the trim will appear on top of the siding. However, if you masked the trim before the siding, the trim will appear behind the siding.

The best way to correct this is to Delete the trim layer and remask it so it appears on top of the siding. This rule applies to everything except doors, windows and foreground. Doors and windows will always the top most layer even if you mask them last. Foreground sits on top of everything.