The junk should settle out in your sump where your easily able to remove and siphon it off.....
I look at the floss and such just as running a dirty filter sock continually.....Bottom line you pick your own poison's basically in the hobby, and a lot really depends on how diligent you are to maintaining your tank and equipment......I guess I'll revert back to why most people convert to a sump.....Yes the biggest "pro" is a place to hide or place your equipment, but probably another big reason is the ease and cost effectiveness of running a sump vs a canister filter; due to the constant maintenance to keep them running "pristine", and the cost of the materials that constantly need changing out. If you keep those materials in your canister, I'd highly suggest if your not already doing so, when you feed to shut the canister filter down. This might/should buy a little time between changing out materials......