I have been using my low side gauge to pull a vacuum, is this wrong?

YES. The low side gauge knows only atmospheric pressure and cannot sense moisture or non-condensables. A micron gauge is a heat sensing device that not only reads atmospheric pressure, but also measures the gases created by the vacuum pump as it boils the moisture. For example, if you were to pull a vacuum on an enclosed bottle of water, the low side gauge when pulling a vacuum will read a perfect vacuum. Using a micron gauge, it will immediately tell you with a high reading the you have a problem in you system.