With pedals held together... Assuming the chains are on the correct teeth of the sprockets, you might have to tension or loosen the nuts on each end of the chains to keep the fins centered. Ultimatly the forward chain is supposed to be tighter than the aft. Also, as you tension the idler cable, it tensions the forward chain.
There is a short instruction in the manual:
http://www.hobiecat.com/support/pdfs/Mi ... Manual.pdf
It is not critical to the function to have them perfectly aligned... get them within a few degrees.