Again I go back to my initial response of 2 towers not needed.....I also question the layout regardless of scrubber or fuge in the first section......Again the skimmer should be fed the rawest/dirtiest water possible IMO.......Again nothing is 100% effective on the first pass of filtering....With that said the skimmer will not process all the water that enters the input chamber.......
Having the skimmer in the first compartment I recommend for 2 reasons.....1 My thinking it would be more efficient in that position, and your thought or theory of issues from micro bubbles from the skimmer......With the skimmer being in that position the bubbles would have more than adequate time to pop. I again go back to the assessment that with proper positioning of the skimmer bubbles could be diffused, or a decent skimmer properly tuned won't give off massive micro bubbles......
Corey I'm not really sure or not remembering that you used 2 bubble towers????? I haven't built mine as of yet......But theoretically I was using it for a different purpose somewhat as well. I personally like to run filter socks periodically, which is a convenient place to mount them.....The during periods where I'm not utilizing them the tower will serve it's intended purpose.....I wasn't a fan or real believer until I built Flowers' sump, and I was trying to blow mad....mad.....mad flow through the sump......I was merely using the only pump I had laying around to flow test, and without it, a lot of bubbles, but the simple addition of the tower allowed me to push that sump well beyond what it would normally flow without one.......
In the skimmer compartment again IMO is wasted......Other than a Coralife skimmer I haven't really read about to many skimmers putting of serious bubbles to warrant a tower......
I'm very behind on the scrubber issue; so Corey you'll have to answer this.....How much splashing bubbles does the scrubber actually produce??? Al you can chime in as well, since your scrubber is actually starting to function and build up????? I would think if your getting a lot of splashing or bubbles from the scrubber than maybe a redesign on the scrubber all together???? I would think you don't want any since this would lead to salt spray/creep which is undesirable by anyone in the hobby......