You can use ISL and 802.1q in the same network. The spanning tree issues arise mainly while 802.1q uses one spanning tree for the trunk link. The BPDU's are by default transported via VLAN1 (Cisco implementation) and the problems could begin when this is not taken into account. Especially in a multivendor network. The above is not nescessarily true when you are using only Cisco equipment. In that case, your 802.1q link can support PVST+ (Per Vlan Spanning Tree), the cisco add-on to the standard.
There are lots of documents about spanning tree on the Cisco-site. When you do a search on spanning tree or PVST+ you will most likely find what you need.