If you dig through the boards you'll find a loootttt of discussion on agencies, pros and cons, people who love em and people who avoid them like the plague.
Some of the more pertinent points:
A lot of independents don't accept agency referrals, because they feel that a lot of agency girls can't be "truthful". Many agencies have strict guidelines on what their girls can do, what they can say, etc, and it's possible they'll tell their girls to give positive references no matter what in order to please clients/get more clients.
It comes to this: Agency girls for the vast majority can't pick n choose their clients. The agency handles all the requests, bookings, screenings etc. The girls pretty much show up/welcome whoever the agency sends to them. In a lot (NOT ALL!) of the cases this means the girls are often forced to see guys they would have rejected on their own. Thus, independents wouldn't rely on their "referral".
As for tipping/upselling, again, this varies greatly from agency to agency. ALL agencies take a cut from the girl's fee, and that can be quite a high percentage (over half) for a lot of agencies. For many the business model is no matter how much the client ends up paying, the agency takes a flat cut, and the girl keeps anything she can get in upsells/tips. So for example, say advertised rate is 200/hr. The agency could take as much as 150-160 of that. It's then up to the girl to upsell/get a tip to make more than the 40-50 base she's getting. However, the better agencies will take a flat fee and leave enough for the girl to be satisfied with the rest of the flat rate, with absolutely no upselling. Keep in mind though that tips are always a good idea regardless of agency/independent if you want to repeat/get better service next time!
Also, beware of the pictures agencies post, especially if it's an agency with a lot of girls. Many lower end ones use stock fake photos, or photoshop photos heavily. Again, research, research, research!