We use HPRT-Cre for whole body KO Some other strain also should be OK like: ROSA26-Cre ACTB-Cre 。。。。 If you want to avoid any possible mosaic expression, you should cross the flox mice with cre mice to generate heterozytous F1. The deletion will also happened on the sperm and egg of the F1 mice, then you can cross the +/- mice with +/- mice to get the real global KO mice.
H*N
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The cre efficiency is not so important here. what you can do is to identify a few het pups that has had the deletion in the germline. By crossing the hets, you can get homos that are 100% mutant.