using studs on my heads

I have a kwik question about my small block. Iam putting new aluminum heads on my 360. The heads have extra thick deck surface (5/8 for angle milling) so I needed longer than normal bolts (actually studs) I installed the studs (just till they bottomed out) and Torqued the heads to 75#.Now looking at the studs and nuts, some have threads above the nuts and some are below the top of the nuts. I was always taught that you should have at least 1 complete thread showing above the nut. I have done tons of imports with wet sleeve motors and using studs and nuts, and I ALWAYS HAVE A THREAD OR 2 SHOWING. Any suggestions ?