Can. Front RCA out can go to channel 1 & 2 of the amp to power the front component set. Then Sub RCA out can go to channel 3 & 4 and then connect the sub to these channels in bridge mode. As for the 6x9 speaker, just directly connect to the speaker output of the HU so not powered from the amp but directly from the HU.
Note that this is provided that your power amp has sufficient power to drive the component set and sub, and can bridge. If your amp does not have enough power to drive the sub, then need to get 1 more mono or 2 channel amp to power the sub. Then channel 3 & 4 can be connected to RCA out 3 & 4 from the HU to power the 6x9.

For SQ setup is usually about using good quality product with minimal distortion and natural sounding package. Many purist even do away without rear channel at all, and SQ I think never uses coaxial at all as coaxial is for economical use. If going for SQ, if I'm not mistaken mostly use active setup whereby each speaker of the component is driven individually by each amp channel and use active cross over connection, as opposed to passive. Sub also normally don't use bridge connection since bridge gives more power at the expense of distortion, so usually driven by a real mono amp. So it's like channel 1 & 2 drives the tweeter then channel 3 & 4 drives the mid, all for front only. Then got one mono amp just for the sub, and not use rear speakers at all.

I'm nowhere near any expert on this and my ears are just very normal and insensitive like regular people but your kind of setup I think is just a normal economical setup, not SQ or SPL. Experts like Howiechoo should be able to explain more on this.