I pretty much go with what the situation requires. I start with Tamiya thin glue, melt & squeeze to create a filler, sprue or plastruct for big gaps, super glue where I don't want shrinkage & Tamiya basic or fine putty for feathering. If I'm filling holes that go all the way through the part, armament holes in wings, etc. I try to use sprue from the same kit.
I do use Mr Surfacer but not too often. I find I need to keep applying it do to shrinkage when it dries. Any filler with a solvent reducer is going to shrink. Don't put a painted model with this type of filler in a food dehydrator to cure the paint. All your filling work will have probably shrunk as a result. Ask me how I know.
I've even use a soft plastic wood that comes in a tub. You can wet your finger & pull it over the plastic wood th smooth it. I use this in areas I don't want to lose detail.
Seems I use whatever is in my line of site to apply this stuff. I will use a exacto blade or toothpick for super glue & filler. My dentist gave me some of his used picks. There is one that has a small beveled end that is handy.
I know a lot of this is repetitive but I hope it helps.