Thanks for listing the info -- I'm surprised there are only 2 fan power headers on the MB (mine has 5)! The newegg reviews aren't that great, so it sounds like your troubles are pretty avearage.
Fans can certainly be powered off the PS from a 4-pin Molex connector (many come with a Molex->3-pin adapter). Usually, that just means they always run at max speed, unless they have a built-in thermosensor control. The stock Intel CPU hsf does have such a control, but the special 4-pin header for the CPU fan also allows BIOS speed control based on CPU temp as detected by the MB. Some MBs/BIOSes allow control of other (3-pin header) fans by varying the voltage output on the header according to a user-selected reference temp (e.g. SYS or PWM) and a user-set fan voltage response based on that temp. I'm not sure what your MB allows, but since there are only 2 fan headers, I wouldn't expect much.
Regarding your temps, an "ideal" SYS temp is probably about 35C or so, but you've got a hot video card in there, so you are not totally out of line. Your CPU warning temp is probably better of at something like 70C, with a shutoff of at least 80C (since modern Intel CPUs automatically slow themselves down at elevated temps to avoid damage).