Yep. There are basically 3 things involved with augmenting -- a kit, a fee to attach the kit and create a slot, and an augment to go into the kit. Whether you've crafted the kit or bought the kit doesn't matter.
Don't forget to have the augmentation kit in your backpack or whatever. It can't be in your cargo bay or you'll be unable to successfully augment your gear.
Weird that augments are the only thing that works this way. Everything else works just fine if you have the mats in your cargo bay.