what color is the smoke? most often: blue = burning oil, thick white = coolant, black = too much fuel.
about replacing the stem seals: when you took the heads off, did you replace one seal at a time (spring & keepers off, old seal off, new seal on, spring & keepers on)? It's very important to keep each valve where it came from. If you didn't, and put #1 intake on #2 or #3 (same deal w/ exhaust valves) it will give you problems. also, the stem seals need to be pushed down so they "snap" in place...if not seated properly, oil can leak down into the chambers.
sounds like you had oil leaking into the chambers anyway, as you said it smoked on startup.
last (and has nothing to do with the smoking), did you use new head bolts? you might be able to get away with reusing the old ones, but new bolts stretch when torqued and old bolts won't torque properly (which will lead to problems down the road).