I can only guess about the Polk HTS 12 since I don't have data for it, but I would guess that two HTS 12 subs would equal a PB-1000 Pro above 30Hz, but not below it. If you want deeper bass, the PB-1000 Pro is the one to get.
As for Geddes and full-range speakers, I wouldn't worry too much about running the mains full range even if you are trying for the Geddes approach. Geddes advises that where it is feasible, so that there are more points in the room that emit low frequencies which further helps to average out room modes. It can also help to reduce any localization you might get from the subs. In a sense, your subs with a high-passed signal to the main speakers would act like that but at a single point instead of two points, so it should be fine.
Regarding the strongest sub, I don't recall Geddes talking about that, but I would guess he would say that the subs should be placed in locations that best bring about their optimal performance, so for example, you wouldn't want to place a sub with powerful deep bass in a location where a null is particularly affecting in that frequency band. So measure the response at the locations where you place the sub, and place the subs that fits their strong suite the best if you are using different subs.