You wanna basically tune each string (starting from the thickes) E-A-D-G-B-E. I'm not sure how your tuner works, but it sounds like when you have the right note, tune it until it gets to the green (I'd read the manual to make sure.) After your done, to make sure its properly tuned, these notes should sound the same:

E-------------------------------------------0------
B-------------------------------0---- -5-----------
G---------------------0---- 4----------------------
D------------0----5--------------------------------
A---0-----5----------------------------------------
E-5------------------------------------------------
...|--|......|--|......|---|......|----|.......|-----|
the same