Timing chain install question.

Yes. Lining the dots up with the crank gear at 12 and the cam gear at 6 actually times the engine at 180* out. You will need to either rotate the crank shaft one revolution, OR put the distributor in pointing to number 6 on the cap. I prefer to rotate the crank one revolution so as to have the distributor in correctly. Either way will work.

I am assuming from your question that you are not going to degree the camshaft. You should.