Here are my General and Class settings, the name of the file should point out which is which
I have to give credit to Benny it are his settings but with a few minor tweaks here and there, because like you I was running into mana problems as well, changing some of these settings fixed that for me. My ilvl is 549 and I have no problem keeping up with full normal geared people, you do have to take in consideration though that you won't be on the same spot in the healing meters every fight, every fight is different and every class has his fights where they will do better or worse than others.
If you start casting late, it could be due to the setting of the number of people that need to be at x % to start healing. You can change this number or when you feel you should already be casting when you are not, just select your tank or use a macro that selects yourself or whatever you like best and cast penance or make it cast penance or whatever instant healing spell you like best and this will also trigger the bot/routine to start. From my experience that is.
When it comes to mana talents I use Mindbender. When it comes to glyphs I use Penance, PoM and Holy Fire, I'd say Penance and Holy Fire are kind of a must-have, PoM you can replace with whatever you like best.
I hope this helps you a bit.