I use disposable chip brushes for staining these days, it makes it easy to work stain into crevices on picture frames, which are my most frequent project. I use a prestain as well, which produces better results than applying to bare wood.
I like the paper towel results very well indeed. Use the corners to apply the poly to those tight spots. I also use disposable clear plastic food cups, pour in enough poly for one coat, then squeeze out all the air and close the plastic bottle. I put a lid on the 2 ounce food container if it has to sit more than a minute. Haven't noticed much thickening as a result, but I also have mineral spirits handy. I used a Forstner bit to drill a recess into a short 2x4 to hold the food container, without it, you WILL get a spill.
Sanding picture frames was no fun until I discovered these sanding pads and the new, flexible 3-M sanding sheets. The sheets conform to the shape of the pad, both the U shape and the rounded end and sanding is done in minutes on picture frame stock. Best $10 investment in accessories yet. I generally sand down to 220 grit, with the occasional quick pass with 320 grit to lightly clip off the fuzz that gets raised by the stain. The 3M sheets are really aggressive, almost like card scraping. Next comes a large paint brush to remove the bulk of sawdust, then a very light rub with a waxed cheese cloth to knock off the dust. For picture frames, I'm generally going for a very high gloss, glassy finish. I highly recommend the sanding blocks, which you can get in angled and curved versions from Amazon or woodworking stores..