For what you are doing, gel stain is fine. For wood like that, you use it similar to regular stain where you wipe it on, then wipe of the excess.
Gel stains are tough to use on fiberglass doors or areas you are trying to leave the all stain on. You have to have a feel for it and it is more artistic to get the look people want.
As far as filler, depending on the size of the area you are trying to fill, you can use a wood fill or for small areas and nail holes, you can use a color putty after you stain.
Downside to wood filler, it will stain differently than your wood, just like trying to stain different kinds of wood with the same stain. You can try to manipulate the gel stain a little Geo minimize the different by leaving a little extra on or wiping more off depending on how the colors look.