I personally wash my pads after every use ( I have about 8 and try to use them all so it is worth washing them every time). I throw them in the washing machine with some dedicated MF cleaner such as MF Revitalizer. Then either air dry them or use the drying machine on low heat in a pinch (washing more than one car).
Same thing goes for my MF towels. I wash them once I get enough dirty for a load (I have enough to be able to wait to wash them), use the same MF cleaner and then dry them on low heat. Stay away from fabric softener is my honest opinion and stick to a cleaning solution meant for MF towels. Also no drying sheets if you do decide to use the drying machine and keep it on low heat or no heat so as to not burn the fibers.
Hope this helps!
P.s. I would not suggest washing them together, I always wash them separately.
Don't beat yourself up on your 06 Accord. 06s Hondas are notorious for clear coat failure. My 06 Civic did it too.
I'd also replace the buttery with paint sealant and I'd start with a 2 bucket kit which would include 2 buckets, wash pads and shampoo. 2 bucket wash is the fondation of swirl free vehicles.
