Both ways of paying the commission are fine, but one shows they trust you a bit more than the other... and are more likely to be declaring their income for tax purposes as well. If you're still interested in them, it's worth asking when and where the other one would want to meet you to hand over the cash - some people have been expected to travel long distances in the wee hours, for example.
One of the reasons agencies are not always popular here is that they can have an incentive to take on people despite not really having work for them. If you get one booking that they otherwise wouldn't have got, it's a result for them, but you may not be happy. So there's no way to be sure, but you can look up how many reviews (and what sort of reviews) their existing staff get, for example.
And don't give up working independently as well unless you've a very good reason to stop.