It’s a debate that’s been around a while – should you/can you apply a finish to a project before final assembly, or should you do it all at the end.
There’s no definitive answer, and “it depends” is the simple response.
The primary advantage to pre-finishing is the ability to apply a finish in hard-to-reach areas – for example, small or narrow parts that are spaced closely together.
The main thing to watch out for when pre-finishing is an area to be glued. By applying a finish to such an area, you essential eliminate a place for the glue to adhere (wood fibers). Try gluing two parts together that have been stained and see what happens.
When you do want to pre-finish, be sure to use a painter’s tape to cover up gluing surfaces. I’ve used the new Frog Tape (it’s green), which is promoted as being better than any previous tape. I have to agree, while it’s not absolutely perfect, it’s the best of its type that I’ve used.
I also recommend a finish-as-you-go approach. Simply apply a finish at each step of a project, after a particular portion of assembly. This gets a bit tricky when you apply stain because you’ll need to watch the amount of time you leave the stain on the project before wiping or buffing.