If you are using a filtration system, then you should just force carbonate your beer. The best and quickest way to filter and carbonate is to keg your beer.
Using the Draft Brewer Beer Filtration System place the Coarse filter into the filter housing between the two kegs.
Run the beer through the coarse filter from the first keg into the second keg.
Replace the coarse filter with the Polishing or Fine filter.
Run your beer back through the polishing or fine filter into the first keg.
Now, just hook up your CO2 tank to the keg, and carbonate. See our article on How to Force Carbonate Your Beer.
If you plan to bottle condition your beer, filtration is not recommended. If, however you really want to filter your beer, you can re-prime the beer by adding a very small amount of highly flocculant yeast I (such as LalBrew® Nottingham English Ale Dry Yeast) to your bottles.