PCIe is on a different pattern to PCI, where they are similar in name they are very different in circuit. PCIe is heavily utilized in the NB where i'm pretty sure the SB handles most PCI... i could be wrong though.
i have a PCI audio card and have not noticed any issue with my performance, but i am running a pretty powerful computer so if it is hitting it, its only a tingle compared to say... only having 4 gigs to my 16gigs ram.
some Motherboards allow a full x16 lane to the primary and x8 to the secondary, PCI is on a different data lane than the PCIe expressway.
if you are experiencing performance issues try upgrading your PSU, as power is greatly diminished in PCIe with more and more GPU's added.
power is diminished with more and more non powered by PSU directly GPU's
powered GPU's by the PSU are not so much a bothersome drain on power and performance.
be sure to have ample floating range, at least 50 to 75 watts above your power demand.
check here (not a strict scale but useful guidance):http://images10.newegg.com/BizIntell/tool/psucalc/index.html