Real estate company in Shanghai

Depends on where in Pudong. If it's near Jingqiao (where most of the expats and Internationa schools) it might not be enough for a good quality 3 bedroom.
If it's near LianYang (or Big Thumb) then you can get a pretty good 2 bedroom in Yanlord or a smaller 3 bedroom in other compounds.

With regards to real estate companies, I'd avoid companies that cater specifically to foreigners as their prices are sky high. Just walk into any local real estate agency (you will see at least 1 on every block) and see if there are any English speaking staff that can help you.
Just a guide for the fees, agencies usually charge 35% of the total monthly rental (if the monthly rental is under 10000RMB). But if it's over 10000RMB/month, then they usually charge the total amount of the month (But then again this is china and everything is negotiable).
Payment terms are usually paid every 3 months, and deposit is usually 1 month (paid alongside your 1st quarterly installment).
You'll have to pay for utilities yourself, including internet, but you can get the landlord or the agency to set it up for you if they don't already have it.

Also, if you plan on staying long term, try to negotiate at least a 2 year lease term. The rent is CRAZY high in Shanghai! The same 2 bedroom apartment I rented 3 years ago is now DOUBLE the price it was!

Hope this helps!