First, congratulations on getting this far!
OK, yes, I would assume that the PL tone listed on the website is more likely to be up-to-date than the one in the repeater directory. If the one in the website doesn't work, try the one in the repeater directory. You appear to have all the data you need to be able to set the radio up right for using that repeater. Here's how you check:
Case 1- You can hear a lot of people talking but it doesn't sound like there's one guy running the show (during a net, one guy runs the show and tells people when it's their time to talk)
1) Wait for a break in the conversation. If the guys using the repeater are good operators, you'll hear the courtesy beep after their transmission followed by several seconds of silence, then a burst of static before the next guy starts talking. The several seconds of silence are the repeater tail-off. During that time, you should see that the receive meter on your radio is still pegged, indicating that you are receiving silence from the repeater (as opposed to a lack of any signal at all). The burst of static is the delay between the repeater turning off (tailing off) and the squelch on your radio closing. It is good operating procedure to leave the tail off "open" for exactly what you're about to do.
2) Hear the courtesy beep and then immediately say your call sign, nothing else.
4) The guy who's "turn" it is next will do one of two things. Either he'll immediately go "Hello *your_call*, this is *his_call*. How are you?. Alternately, he may say whatever he was going to say to the other guy who was already there before acknowledging you. He will basically indicate it's your turn to talk one way or the other.
5) You say something to the effect of "This is *your_call*. This is my first time transmitting, are there any problems with my audio? I didn't catch who else was in this conversation, so back to *his_call*". The idea is to a) give your call since you're required to on your first transmission, last transmission, and once every 10 minutes in between b) indicate you're trying to confirm you're doing things right and not having technical difficulties, and c) make sure you pick someone to talk next. If you've noticed the conversation is going in a circle and you actually do know who goes next, AWESOME, turn it over to them. If you couldn't figure it out, send it back to the guy who acknowledged you.
6) If you want, hang out and talk to practice things like using the mic properly, etc.
7) When you're done, tell the guys you're leaving, say your call, and (usually) indicate what you're doing next. For example "clear and listening" would mean you're done talking but will continue to listen to the radio. "Clean and out" means you're done and won't be listening to the radio anymore.
Case 2- You can hear people talking but it sounds like there's one guy running the show (this is probably a net)
1) You will need to "check-in" to the net. There's generally a mass check-in period at the beginning of the net and then the net control will ask for additional check-ins every few minutes.
2) When the net control asks for additional check ins, say your call sign and wait.
3) The net control will usually let 3-5 people say their call and then will repeat the calls back to make sure he heard everyone.
4) If he does not repeat your call, he will eventually say "OK, is there anyone else who wants to check in?". At that point, say your call again. The most likely reason for the net control to miss your attempt to check in is that you "doubled" with someone else. This means you and someone else transmitted at the same time and the repeater only listened to whichever of you was stronger.
5) The net control will acknowledge you and put your name on the bottom of the list. They might also ask for things like your first name and location.
6) Wait for the net control to tell you it's your turn.
7) Say something like "This is *your_call*. This is my first time transmitting. How's my audio? Back to net control."
8) Wait for net control to tell you if your audio is ok or not. If it's not, they'll usually suggest how to fix it (9 times out of 10, this is get your mouth closer to the mic and stop shouting).
9) Then discuss whatever the topic of the day is.
10) Finish with "This is *your_call* back to net control"
Case 3- You really don't hear much of anything
1) Listen a minute or so to confirm you're not interrupting something
2) Key the mic and say "This is *your_call* for any station. Can any station give me an audio report?"
3) You should actually hear your own courtesy beep and then the repeater tail off. Failure to get a repeater tail off indicates you have a technical problem.
4) Hopefully, someone goes "*your_call* this is *their_call* your audio is clear. How are you doing today, I don't think I've heard you before."
5) Talk for a bit for the practice.
6) Finish the conversation with "*their_call* from *your_call*, have a nice day, clear and listening" or something similar.