I don't recall this information being addressed in the comics, much less in the cinematic universe-Nolanverse. According to this reference he earns 80K as a butler and another 150K as a Wayne State manager.
A basic google ("butler salary" keywords) search showed that
A butler usually earns a salary between $50.000 and $150.000 annually, plus benefits. We realize that the salary indication is very broad but it is what it is. A butler can be a live-in or live-out employee.
source: International Butler Academy
So the information in the picture seems to be "in range".
The payments can be done via a third party, or even Alfred "pays to himself". Basically, if you have kids you may want to make a will in case that (God forbids) something happens to you. There is something called a trust (and probably I may upset lawyers for oversimplifying) but in case that you want to leave everything to your kid, but don't want to leave him a big amount of money when he is not old enough or mature to spend it wisely, you leave it to a trust or third party to administer it. Alfred or some lawyer can be that third party (Alfred could have been named in the will both legal guardian of Bruce and manger of the trust for Bruce's inheritance). Since the Wayne trust him enough to make him legal guardian of Bruce they could very well trust him to administer Bruce's wealth and be honest when paying himself his own salary.
Alfred may own part of Wayne enterprises. After all, buying stocks of the company seems like a reasonable way of investing. If the Wayne left him any participation of the company(ies) on their will is unknown on the Nolanverse. Also Alfred could very well be one of those "various charitable foundations, trusts and so forth" that Bruce uses in Batman Begins to reclaim control of Wayne Enterprises.