To 'Base Up' refers to one of three things.
1. The application of hand sanitizer (from the base to the tip, hence the name) to ones genitals before or after a particularly questionable bout of intercourse (though a post-coital 'base up' is less likely to result in unwelcome friction).
2. In reference to the sexual encounter itself, whereby you engage in risky business and will likely require the application of 'Base Up' in the near future.
3. As a noun referring to the sanitiser itself.
"I didn't use a condom, better base up"
"Should we base up before going to the clubs?"
"Who used all the base up?"