There are a couple of links you may want to look at for background:
Re. which version of Flash will be used ... there again there are changes (coming). Google plans to block all NPAPI plugins: Saying Goodbye to Our Old Friend NPAPI. So that won't be an issue in 2014. Quite sometime ago, I recollect that if two plugins were available, they would not have the same "priority" and so the one with the higher priority would run. For an oldish view on the topic, look at Why are Two Flash Player Plugins Running In Google Chrome?.
Re. which one you should disable ... I'd suggest not bothering unless you have a problem with the PPAPI one. It's not that both would be consuming resources when you watch Flash content.
(For Linux users ...
Adobe will only provide "security" updates for Flash on Linux. So 11.2.202 was the "final" full version of the NPAPI version.
Google, in collaboration with Adobe, will provide the PPAPI version of Flash for Linux.)