Manually Leveling Your Bed - MatterControl

I hear some people saying to NOT use the auto leveling feature in MatterControl, and others say it works fine. I've had mixed results. Sometimes it works well, and other times; not so much. I've looked around on the forums for articles that explain how to level an R1 Robo, but I can't find any. My heated bed has 3 magnets; 2 at the bottom (front) left and right corners and one at the top (back) middle. My heated bed is on smooth rods going through some bearings. I don't think (based on the design with the magents, etc) that the bed really isn't meant to be leveled by itself. I think it is expecting the software to auto-level and do math calculations to determine where to sink or raise at different parts as it prints. With rounding errors, etc. I just don't see that as being very efficient.

I own a dial guage and I have a general idea of how to level it with that. My question is; exactly how do I do this? In MatterControl, under the Configuration tab, there is an auto calibrate section. You can disable the auto calibrate and change the settings manually, but they don't seem to hold. As soon as you send the next print, it changes those settings. I'm a little confused. Any help would be appreciated. Thanks. - Jon