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I see no reason both can't work together getting the "best" of both worlds.
The more I read up on these I think that Shawn AND Snake are right. Running both can give you the best of both worlds.
Habs you can do a skimmer section, fuge with scrubber, then return section. I think a fuge without macro but with live rock would work real nice. Like Snake said you can dip the screen off in the fuge to release the pods that would then take hold in the live rock you have in there.
Either way you do it I think that this will be a nice setup, and I like that you are taking you time and planning it out well.
BTW, NOW I think that I am going to do a scrubber with live rock in the fuge. LOL Anyone got a good like to some plans?