To answer both questions - yes, just run the fuge in parallel with the sump, not in series.

Flow from tank is split - about 2/3 to the sump (with skimmer) then back to a return chamber, the other 1/3 of the flow goes to the fuge, which then also dumps back into the return chamber - any pods that fall in get pumped back to the main tank without going through the skimmer. The pump does very little damage to pods.

Mentioned the mangrove - I just got it because I like it - it doesn't contribute appreciably to cleaning - the algae is much more effective - but the mangrove is a neat plant.

you can and in fact eco systems sell them now incororated into one unit. it kind of defeats the purpose of an eco system running the skimmer full time, i suspect they are doing this as a way to sell units to unconvinced customers.

there are times i wish i had a skimmer i could flip on for a few hours so im not totaly against them, i just think most people overskim their systems.