Tune it like an upside down guitar.   So your guitar goes E A D G.  Your mando goes G D A E.  Easy to remember that way.   

Do the strings *sound* flat, or are they *actually* flat.   What does your tuner tell you?   And is it flat when open, or only when you're fretting?  If its the latter, you can adjust intonation by adjusting the bridge.  My mando is almost half a step sharp 12 frets up the neck.  I've got to get that fixed.