Hey Gail,
Well since you're talking about September, don't worry. Blackflies are a spring problem, not fall.
We camped mid May at Bon Echo last year. Its about 1.5 to 2 hours south of Algonquin. We had nets, but didn't use them much. I might just be lucky, blackflies don't seem to bother me much. They 'bugged' Kate a tad, but we had fun with the hold 'net thing'...
If your looking for remote, but taking your tear, you'll have to choose one of the parks off the highway in Algonquin. Pog Lake is pretty nice. Lake of 3 Rivers and Mew are close to the highway. How about Bon Echo? It will be quieter, excellent for canoeing and kayaking. Great park. I have lots of photos of it on my site.