Sarah,
802.1q does not support PVST+ natively, however Cisco switches do support PVST+ over 802.1q trunks. So with "all" cisco switches and PVST+ (which is the default) everything will be ok.
When you use cisco switches with non-cisco switches, you must use a 802.1Q trunk, that will support CST (Common Spanning Tree), with 802.1Q into a CST region, only one instance of STP runs over the native VLAN, and one STP topology is used for all VLAN's.
HTH>