I am thinking that your problem is as simple as how out of the tune the bass is. The tuner has no idea which string you are playing. It just knows what frequency is going into it. So when you are playing your "E" string and it says it is a "C" then your top string is tuned to "C" and you need to adjust accordingly.
to get it in the ballpark if you are new. It will at least let you compare what your string should sound like compared to what your string does sound like. When you get in the ballpark your tuner will be much easier to use.
For example if you get in the ballpark and you play your "E" string and your tuner says "D". Then you simply need to tighten the string up a little bit to "E".
The notes go in alphabetical order. A - B - C - etc.
Sorry if some of the advice I gave is a little insultingly simple. You said you are new and the other posts seem to be questioning the tuner when it sounds like operator error to me. Hope that helped.