Parts of Pasig and Pasay are also relatively nice and aren't too far from the places you'll probably be going to, including Makati.
Rental rates will be cheaper and public transportation readily available thereabouts, although especially at peak times, don't expect to get anywhere fast--Manila's currently listed as the most densley populated city on planet earth. Combine all the people, pollution and the use of leaded gas, and it can get pretty grimey. I'd plan some trips outside the town--Baguio, Subic--even Cebu City and it's outter regions by air isn't too far or too expensive and the break from Manila mania may be welcome.
You'll most certainly get a much better rate if you have a Filipino friend take care of the arrangements, if that's feasible, but you probably know that already.
If you're going to be carrying a lot of cash and credit cards around Manila, I'd advise going by Triple A auto or a dept. store and picking up a cotton money belt for under your jeans, using that and just keeping a couple thousand pesos in a wallet, tops. I always secure my passport and retain paper copies too.
I've never been robbed, but my wife has family in Makati and while it's generally safe, even they are very careful.
