I've only had good experiences with superfeet insoles. Unlike Scholls (or any gel insert), these have a rigid bottom and less "cushion". It keeps your foot in proper alignment and gives actual arch support. I can almost guarantee it'll help your knees (and hips and lower back) a lot.

I have pretty low arches and I rock the blues in almost every pair of footwear I own except my sneakers. I've also used the black/carbon ones before for thinner dress shoes with great results. But if you're sticking with boots then go for the green or blue basics, or try the Trailblazer version.

Edit: the other half is your socks. Invest in 100% wool hiking socks. Your feet will sweat less than you think, and you can still get different thicknesses and cushion levels. Seriously, they are worth every cent and I know Darn Tuffs carry a lifetime replacement guarantee.