"do you", but I would not use a comma here.
(In fact, the version with "you" is possible in colloquial speech, when "only" can mean "except", but I think this is very unlikely to be what you intend.)
Mr WordyIn fact, the version with "you" is possible in colloquial speech, when "only" can mean "except",
A: Am I doing this right?
B: Yeah ... kind of ... only after you start up the generator you plug in your extension cord.
(i.e. he did it right except that he forgot to plug in the extension cord)
Only after you start up the generator, plug in THE extension cord.
Marius HancuOnly after you start up the generator, plug in THE extension cord.
Hmmm. This doesn't sound natural to my ears.