Here are the basics:
How to fish with more than one fly - There are several situations where tying more than one fly on your tippet makes sense. We go through a few and show you several methods of rigging and fishing more than one fly. - Global FlyFisher
Casting Doubles | Riverwood Blog - Fly Fishing Gear & Guided Fishing Trips in Oregon
That should help with two fly setups.
No need to use an indicator when fishing a dry fly and a nymph, the dry fly should act as a strike indicator. If the fish takes the dry you'll see it, if the fish takes the nymph the dry should twitch, bob, or sink. The only time you might use an indicator with a dry is if you are trying to sink it, sometimes sinking a caddis or ant is very effective.