Fellow uke noob speaking: I use this programme when near my laptop; otherwise I borrow my friend's clip-on tuner. I'd definitely recommend getting a clip-on tuner - you can tune wherever you are and since they tune off vibrations it doesn't matter if you're somewhere noisy!
If you have a microphone on your computer, I suggest AP Tuner if you're on a Windows PC. I use this for my all my instruments including my guitars, my basses, and my trumpet.
As the others in this thread have said, from thickest to thinnest the strings go: E, A, D, G. As for being too deep, a bass is meant to sound deep so that might not be the issue. Unless the string is actually making buzzing noises because it's bouncing on the fretboard, you should be fine with it.
When you're tuning your bass, your goal is to get it as close to the note it's supposed to sound like as possible. So if you can use the tuner I sent you, the note should register as an E1 and then there is a needle pointing at how far away from the center the sound is. This is pretty much the same concept for all the tuners I have used. If the needle is to the right of center, it means the sound is too high or "sharp," and that means you have to loosen the string with the tuning peg. If the needle is to the left of center that means the note is too low or "flat," and that means you have to tighten the string with the tuning peg. Play around with it until you figure out how turning the tuning peg affects the sound. The only thing is, don't go to the extreme of tightening the string because, at least for guitar, there's a chance for the string to snap. Now a bass string snapping sounds like a really bad experience and I would not want that to happen. PM me if you want me to explain further/have more questions. I'd be happy to help.