Best cooling config

[Larkin600]

First off I'm currently using an Ultra m998 tower which have limited options as for as trying to setup the Corsair H50. I've had the H50 for almost a year now and it's a great cooling unit. Every since I had the H50 installed I took for granted that it would work best in the exhaust configuration. And it has but my temps aren't quite as good as some of the folks I'm reading about. So, I decided to try the H50 as an intake to the cpu. My computer is responding like it never has before because of the cooler air blowing onto the cpu area. The problem now is that I only have one fan in front and a place for a fan in the back. Under normal circumstances the flow should be intake from the front and exhaust from the back. Okay as I stated earlier this is the way I had my system setup in the beginning and it worked okay but changing it around to having the H50 as the intake instead of the exhaust made a big difference in the way my computer respond. The only thing is I have the front as the exhaust also which means my temp will probably suffer because of warm air being blown over the motherboard and warm air probably not being moved out of my case. There are two more vents in the side for vga fans etc. Could someone please help me with configuration? Do I have any choices or do I have to live with the old config of front intake and back exhaust. At the moment my temps are #0 45c, #1 46c, #2 47c, #3 42c and this is at 35% load because I'm downloading something. My system is also overclocked at 3.360.04MHz. does these temps seem bad?

And I fell to mention I'm using Shin Estu thermal paste.