In general, for a node that isn't operating in Hidden mode (page 223 of SR4A), you perform the following:
1. Access the Node, your Access ID determines the type of account you have access to. If this is some Sammie's comm-link that you're fighting, odds are you don't already have a real account, so you get dumped in the
Public sector of the node (SR4A, pg. 225).
2. If you're in a hurry (because they're shooting at you, or your buddies), you then attempt to "Hack on the Fly" (SR4A, pg. 235), this is an extended Hacking +Exploit (target's Firewall, Complex Action) test. That is, each initiative pass, you build your Hacking (skill) + Exploit (program) die pool (+2 if in Hot Sim VR, -1 per previous test if your GM uses that rule). The threshold is equal to the target's Firewall, meet or beat that, and you're in. This gives you a
User account (SR4A, pg. 225 again). For a
Security account, increase the threshold by +3, for an
admin account, it's +6 to the threshold (SR4A, pg. 235).
2.a. Each time you make your Hacking + Exploit test, the node rolls on an Analyze + Firewall (hacker's stealth, reflexive) extended test. If it gets there, whether or not your in, the node goes on alert (SR4A, pg. 238). What happens then is GM's call.
3. If you're not locked out, you now have access at the level appropriate to the account you choose back in step 2, exactly what that account can do is up to the GM to decide, but a few logical things present themselves. If you want to mess with the person's cyberware, you need to know if it's slaved to the comm-link, if not, then you still need to hack into that (good luck, thread
here on that).
3.a. If it is slaved, and the GM agrees that you have the right type of account to give a command to the cyberware, see Unwired, pgs. 55 and 102 for more.
That's really about it, assuming no alerts, and alerts are largely in the GM realm once you trigger one. There's a lot of other things you could do, such as spoofing commands and the like, but I'll leave that for the matrix experts (and please, matrix experts, correct my simplified understanding shown above as necessary).