You might consider replacing the rotten wood entirely.
After finishing, unless you've removed all traces of damp wood, any dampness left will continue to dry out and the wood will shrink. It will move away from the filler in places, the paint will crack and rain water will get into the gaps and the rot will continue.
Even more expensive than auto filler is this remarkable stuff...
http://www.youtube.com/user/MediaWayUK
Very satisfying finish but the drying out issue is still the same as for auto filler - they suggest an 18% moisture content or below for any remaining wood.
Good luck...
Peccavi
May 2009
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