I learned MySQL alongside PHP, and Perl separately. I don't remember hitting any traps or gotchas when I started combining the two.

Managing & Using MySQL (O'Reilly) was a useful resource, though, even though its focus was on the interactions between MySQL and generic external sources. If I recall correctly, it does have a smallish Perl specific chapter.

All in all, I think if you've a handle on both separately you won't find any surprises or troubles using 'em together.