I tend to leave off really small decals, especially if the color of the decal and the color of the model where they would go are close, such that you would hardly see them.
I've only done a few two part decals. For order, you want put the decal that is in the background on first (my guess, the bigger one). I remember I waited a day before putting the second one on, so the first had plenty of time to dry and settle.
Good Luck,
Paul