The mounts themselves don't determine how low the rear of your truck will sit.. since the ideal setup is mounting the bags fully compressed when laid out. How low you sit will depend on your notch/link/etc. The bags just lift you up and down from the lowest point.
The different brackets (Over Axle/Behind Axle/Behind & Under Axle) are just different options depending on the room you have, the look you're going for, and more importantly.. the less you want to cut the bed. With the Behind & Under Axle brackets you can have the upper bag mounts/crossmember lower than with the other two bracket styles.. meaning less cutout in the bed (depending on wheel/tire size though.) The Behind & Under Axle brackets can also double as your lower link bar tabs under the axle (2.5" width)
Here are some pics of a Hardbody I did a while back..
You can see how I didn't have to cut out a huge section of the bed for a bridge type setup with over the axle brackets.
If you have any other questions, or need a set of brackets hit me up anytime -
Ricky@WhyNotFab.com
Hope that helps some.. good luck.