Hey, chemi pure can go anywhere as long as water is passing through it.Carbon works best in an upflow reactor but media bags is better then nothing. The output for skimmer can also just about go anywhere here are a few things to keep in mind though.
The output will produce some micro bubbles, you don't want that in your tank so try to have the output away from return pump a bit. Depending how your setup (internal/external) you want output as straight and clean a run back to sump as possible. You don't want the output being obstructed by anything(pump body, side of sump, baffle) that can possibly restrict flow and make it hard to get dialed in correctly, leave yourself a couple inches from anything. When you make adjustments make very tiny ones and wait decent periods of time between adjustments.