mikegee,
you need to add a regiment of ear training into your practice time. if your having trouble tuning by ear, i can only imagine the trouble you run into trying to play a song you hear on a cd/radio... same principle..
there are many methods you can use to tune your instrument, i will recommend this one..
fun stuff, untune your bass and (with it unplugged) hit the E, B, F# what ever that telephone like string is on your bass, place your lower earlobe (head,chin,cheek, whatever) against the horn of the body, you will feel the hum of your bass.. similar to tuning forks.. you should never have problems tuning once you train your ear, also it is very affective to train your voice, and use this tuning method also.
using alternate tuning you can turn a 4 string bass into a nightmare mass confusion but fun playing bass, with extended bass tunings you can really get crazy.. Vic Wooten live does alternate tunings while hes playing a song and comes right back into tune, its absolutely amazing.!!