First off you should identify if excess PO4 is really your issue, otherwise GFO would not be a great option. Take an accuracte test of the level, Hanna meter is by far the best for this as most liquid kits are junk, you want to be at about 0.03 ppm. As mentioned earlier too low of PO4 will cause issues as some is required by corals. It's hard to completely eliminate though (and through feeding you'll add more), where most people get into trouble it by lowering PO4 too fast, whether it be too much GFO being used or too fast of flow through the reactor. Make sure to take note of both things, and as mentioned run less than initially recommended. I'd start with no more than 2 grams per (actual) gallon, assuming you're using Bulk Reef Supply GFO (many manufacturers are similar but some are not).
You want to make sure to have efficient sand sifting going on as well. By this I don't mean go out and buy everything with the common name "sand sifter" such as gobies and stars. Bristle worms and other small critters are the best, and a few larger animals here and there such as nassarius snails work great.
Keep in mind that SSB (shallow sand beds <2") should be siphoned on occasion, which will help reduce nuisance algae growth.
As Chris pointed out skimmers will not interfere whatsoever with GFO nor the other way around. Skimmer pull out DOC's (dissolved organic carbons) prior to them being broken down. Although GFO will remove other things it's primary focus is to absorb PO4, which it is very efficient at doing.
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