That sounds as good a system as any. It it works for you, it's right...
Ah, you said you're going to count metres. Well, you could do that with toggles, taking account of your pace count to move the toggles when you've counted enough paces for 100m, but the alternative is to use the toggles to count paces, and convert to km. Again, whichever works best for you.
The other issue to consider is how long your navigation legs are; 11km (10km + 10*100m) is quite a long leg to measure accurately with pace counting... (depending on terrain).
You can also count down with the toggles; when you start a leg, measure the expected distance, set the toggles to that value (whether metres or paces), and count off the distance as you walk. When the toggles reach the 'end', you should be at the end of your leg. This saves you having to remember how long the leg should be, since you only measure it at the start.
A friend has her toggles on one cord, tied to her rucksack strap at the top, bottom and middle, with km in one half, and 100m in the other. A bit like an abacus.