When your Asus software monitors fan speeds it does so by means of the 3-pin motherboard headers. This is what sends data through the Winbond chip onboard that gives software utilities the ability to monitor things like this. If your fan has a three wire connection you should be able to search around and get a converter that still allows you to use the standard Molex connector for fan power (a good thing) but will also include a small yellow wire with the 3-pin connection for the motherboard. This will let you monitor fan speeds and such. If your case fan only has two wires going to the Molex connector, you're stuck and won't be able to monitor the fan.
As a side note, be careful with that "Fan Only" plug used by Antec. If you're happy with it great, but I don't generally like a power supply making the decision as to how fast my fan should be moving when it computes this by a small thermal probe inside the PSU itself. I usually add this plug to the grouping of unused wires that I zip tie and stash out of sight.