The patch levels will be dramatically affected by the amp modelling that you're using. If you are using the "Pre" modelling and the DT's power amp topography & NFL, the levels will differ quite a lot, particularly if switching between class A and class AB. The different pre amps all have different gain structures and they all hit the power amp at different levels too. Think of it this way, if you put a real 85 Watt Fender Twin Reverb next to a real 30 Watt VOX AC30 and check out the volume difference, you'll be amazed at just how loud that AC30 is. The physical differences in the circuitry are responsible for this and the Pod HD with DT amp is duplicating those differences.
It gets much easier to balance levels when using different amp models if you use the full amp models in the Pod HD and select class A Topo I on the DT amp for all patches. This means that the amp tone is a finished product going into the DT amplifier and using class A Topo I will minimise the effect of the DT power amp on your tone. You can then balance patches using the channel volume. Don't be afraid to tweak the deep editing parameters on the amp modelling to get the tone you're looking for.
Cheers,
Crusty