If you’re playing with a singer, it’s ideal to change your tuning to fit the singer’s vocal range. In this case, it’s perfectly fine to tune the shamisen down to the low key of A all the up up to a piercing key of E! (Though please note that the strings have a higher chance of breaking up there)
Because a specific key will be necessary, use an electronic tuner to set the key of the ichi no ito (thick string). However, the other two strings can still be tuned by ear (as described above) if you wish.
And that’s about it! There’s no real secret to tuning the three strings. All it takes is a little practice and confidence!