I don't quite comprehend what you're after. I gather you don't want to use, say, hotbar 1 in PvE and hotbar 2 in PvP. Apart from that, you can create macro that sets certain skills to certain slot in certain hotbar. So make one macro that sets your pve skills to your slots 1, 2, 3, 4 an 5, and another macro that sets them back.