For those who don't want to be bothered by actually going somewhere, there is always Sulit for you. Some musical instruments there, I hear, are sold cheaper than what you usually see at music stores in malls.
However, if you're adamant that you must test your guitar's cool xlr to 1/4 or want to be taught to tune your new violin, then here are some areas/shops you may want to visit:
Go to the vicinity of Raon in Quiapo (or you can start from the Sta. Cruz area going to Quiapo). Just ask whoever to direct you to the streets where music stores selling musical instruments, accessories, amps and speakers are. My relatives even buy their flutes and saxophone from there because it is cheaper.
Basements of malls usually house the music stores selling instruments and accessories.
Sta. Mesa in Quezon City is also popular for having many stores that sell musical instruments.
And then there are RJ stores that are sure to offer the best of quality you can buy.