It will really come down to your convenience. How big is your batch? If a small one, go ahead and deseed first. For large batches, though, I find it easier to deseed after they're already dry. I dry at 90F to keep the seeds viable.
To correct what pixelatem said, the heat of chiles comes from the placenta, not the seeds. So removing seeds only does not detract from the heat of a pod or your powder. This is a common misconception - the seeds only seem to be hot because of their proximity to the placenta.