I don't think there is anything wrong with using two at once. There's an old thread here somewhere where people discuss their experiences combining the two; try searching for Al Manning, perhaps. The discussion was about Al's BPDE, or Basic Psychic Development Exercise. In Ishtar you sensitize the chakras with the hands and the entities, whereas the BPDE is all in the mind and the person.
That said I think it also depends on your personal makeup. For me, one or the other worked better, and I can't say I did well with both at the same time. I got better results with the Middle Pillar in general than the BPDE chakra exercise, so I dropped the latter. Right now I'm working with a five-chakra system (reminiscent of the MP) that works better for me than the MP, which in turn seems less effective for me now.
So try both, and if they both work great. If not, feel free to stick with what resonates better.