Hi, normally onboard ports are a bit faster (20% or so) just because they don't have to compete for the PCI bus. Only in the case that your onboard USB2 chip is VIA or ALI AND your PCI card is NEC chipset based I would recommend installing it, because it has been proven that NEC is USB2 host chipset king, with a lot less compatibility problems than the other solutions,... and also faster in general.
Regards
FTC