When I'm going for toothy critters like Spanish Mackerel and Super Small sharks I prefer using leader material, a few inches or feet at a time.
When fishing for snook and other fish that aren't as toothy, but there is a lot of abrasion around I prefer to use a main line product, and put a few yards on at a time.
As for knots, a double uni works well when joining mono to flouro, but for braid to flouro I prefer a slim beauty knot, although there are other knots that work as well and are probably easier to tie.
I never allow a knot to pass through a level wind found on a baitcaster, it is very detrimental for both the knot, and the reel. For those instances, I'm only using a rod's length of leader material of any kind.
I've also found that under high stress fights, with larger fish, Flouro works better as leader material when tying to braid, because especially with a continually cinching knot like the double uni knot as an example, the braid will literally continue to cut into the mono until it has cut through it.