You can print via USB to any Makerbot clone printer directly from Makerware, there’s no reason to use a host program. (Astroprint and Octoprint have recently started beta support for Makerbots/clones if you’re interested in that.) If you do want to use USB printing, be sure to update the printer firmware to a recent version of Sailfish to get some important USB bug fixes.
RepG is old and broken, and it confuses many people that the clone manufacturers still recommend people use it for slicing. Tons of people run FlashForge/Monoprice, Wanhao, and CTC clones using Makerware. It’s still one of the best options on the market for dualstrusion printing. If you want something nicer than Makerware, Simplify3D is awesome and has good native support for Makerbot clones.