If you’re using line level (with Apogee) you’re bypassing the Preamp.
Otherwise, if you’re using instrument or mic, and you raise the gain (in Apogee’s Maestro software), you are increasing the volume of the Preamp.
Can’t comment on how it works on your particular audio interface.
I use HOSA cables. But I’m a hobbyist and don’t run a professional studio. If I were to upgrade my cables I would go for something like this.
http://www.amazon.com/Monoprice-Premier-4inch-16AWG-Plated/dp/B001UJEKZ6/ref=sr_1_1?ie=UTF8&qid=1432225383&sr=8-1&keywords=TRS+to+XLR
I don’t feel the more expensive cables justify the price.