The clutch and stator covers both have a fiber/paper gasket that will most likely rip apart when you remove the covers. The stator insert (round piece) has a rubber re-useable gasket. For the valves you just have to remove that so you can turn the engine by hand.
The middle gear cover must come off before the entire stator cover, it overlaps. It also has a fiber gasket that will rip apart. I used Yamabond 4(any yamaha dealer will have it) to re-seal it because the local dealer didn't have any gaskets. Been fine for months. You shouldn't use sealant alone on the stator, since it can bind the starter reduction gears(cover would ride too close to the case).
Since you have new covers, you'll have to change the stator over...make sure you have a proper philips screwdriver for the 3 stator bolts. It's a big one. An impact screwdriver would be even better, but I cracked all 3 of mine loose with (iirc) a #3 philips. Just as I thought it was about to round off they came loose. If it doesn't seem to fit quite right, DON'T use it. Go get a proper one.
You can change the clutch cover without any oil leaking if you have it on the side stand. For the stator side covers, you either have to drain the oil(catch in clean container if you plan to re-use it), or tilt the bike the other way. I put a jackstand under the right side peg and carefully leaned the bike on the "wrong" side so I could remove the covers without messing around with the oil. If you're doing both sides might just be easier to drain it.