I use the more solid flower stamp first in the lighter color ink and then the "outline" flower stamp over the top with the darker ink. Or you can stamp off once or twice for the first layer and then stamp the outline one without stamping off.
And I always stamp the stem first and then line up the flowers. I use the clear stamps so it lines up pretty easily. Maybe a stamp-a-ma-jig would help??
Here is a card I did a while back with the stamping off technique...
Thinking of You in Blue IC300 by mandypandy - Cards and Paper Crafts at Splitcoaststampers
Hope that helps you out some!