It will be fine, as long as you don't have any PCI cards installed. Basically two slot and 3 slot means it takes the space of 2 or 3 cards. So in your case, if you had a 2 slot card, it would take up the PCI-E X16 slot space AND the first PCI slot space, meaning you could only use one PCI card. They still only plug into the PCI-e slot, but are that big, they cover the adjacent slot, rendering it unuseable. A 3 slot card would cover 2 adjacent slots reneding them unusable, which in your case would mean you couldn't use ANY of your PCI slots. Your PCI-E x1 would still be useable, if the case allows.
Hope that helps.