If I want a 7-10mm final bead size I start with a 2-3 mm base, yep. You need a 2-to-1 ratio, minimum, of clear to base if you want a full encasing. So if you do 1 wrap of your base colour, you'll need at least 2 wraps of clear to get good coverage. It will stretch your base bead wider as it melts. That's another reason to start with a tiny cylinder - if your decorations are already on a fairly wide base (like, 4mm), they won't distort as much when your clear is melted later.
Heating just the clear takes some practice getting to know the flame and being able to judge the heat level of the glass. But basically what you want to do is think of the flame as a surface, like a jet of water, that you can dip things into partly or completely. Hold your mandrel horizontal and perpendicular to the flame, then just touch the bottom of your bead to the top of the flame, and watch - it'll go molten in that one spot, but the base should stay stiff. This lets you spread the hot clear over the base like frosting, without distorting your decorations. It definitely takes practice - don't give up!
Here's an example of my encased rounds. These are 10mm from hole to hole and 13mm in diameter. They're encased twice, so the starting base was VERY tiny!
-Heather