Sanding.
One of the things that comes with cutting practice is smoother cuts that require less sanding. When I started out I used a variety of things to sand the inside of fret cuts; needle files, emery boards (for filing fingernails), sandpaper, sanding blades. Now a few years in I almost never use them. If I notice a part that needs sanding, I am as likely to put it back on the saw to clean up the cut as actually sand it. To remove the blade fuzzies from the back side, I use a mini butane torch to burn them then they sand off really nicely.
some of my favorites were
https://www.amazon.com/SC91262BL-Scroll-Sander-4-Inch-Assorted/dp/B00CTGMOT8
https://www.amazon.com/Olson-Saw-SC42101-Scroll-Files/dp/B000N6K39O
https://www.amazon.com/Lumberton-12301-Sanding-Sticks-Standard/dp/B0039ZB24G
Stain
I don't stain often, so I am no expert. However, I find that if I stain the front and back with a really wet foam brush that most of the little frets get filled in. I think I took a q-tip once and got all of the little spaces, but it was too much work and the finished product wasn't better. From time to time I will stain a piece of plywood, then cut my project.