The general rule of thumb is to use natural brushes, sometimes referred to as China brushes, for all oil-based finishes (including paint), and synthetic brushes, sometimes referred to as nylon brushes, for latex, acrylic or water-based finishes. Rollers and rags can work for either type of finish.
Because these are the top coats being applied, you'll want them to look as good and as smooth as possible. The best conditions to apply are when there is as little dust or other airborne particles as possible. Clean your work area as thoroughly as possible and allow some time for the dust (literally) to settle. Consider using a dust collection system or air purifier.
When applying a finish with a brush or roller you may notice some bubbles pop up. Don't panic. Many times these will settle out as the finish dries. If it's a problem, simply use a rag to wipe it down. You can often avoid this by applying a thinner coat. Also, shaking a can of finish will certainly add bubbles, so try stirring instead.
After the first coat dries, you'll need to either sand it with fine-grit sandpaper (220 grit) or use steel wool. You may have heard to only use steel wool, but many manufacturers recommend either one. Just be careful not to deeply scratch the finish and certainly do not sand off the finish to the point where you reach raw wood. Wipe off the dust created and apply another coat. A couple of coats are usually enough, but you can apply additional coats (more wiped-on coats can be applied than brushed or rolled) to create a thicker and more durable finish. Try not to exceed four or five coats of finish.