I built my PC around 3 or so years ago, with the following:
Intel Core 2 Duo E6750 2.6ghz
2 gigs of 1066mhz DDR2 Corsair Dominator
I recently purchased 4 gigs of 1066mhz DDR3, my question is, how do I know if I'm getting any advantages of my ram upgrade? Things like 3DMark06 focus more on graphics and CPU right? My 3DMark06 numbers are actually less with the DDR3. I was running the DDR2 at 5-5-5-15, and the DDR3 is running at 7-7-7-20.
An older generation of memory tends to have better (lower) latencies than a newer generation of memory running at the same frequency. Since you used both DDR2 and DDR3 I assume your motherboard supports both technologies (but not both at the same time). In order to get better latencies you would have needed to get a faster DDR3 memory kit.
You shouldn't notice any speed difference between the two kits with pretty much everything on the computer. Differences in memory performance tends to be of little importance for all but very few programs. The most commonly used of such programs I'm aware of would be compression/decompression. You might notice a slight increase in the time taken to run compression/decompression tasks.
Newer systems can take advantage of much more mature and faster DDR3 modules than the original quality of DDR3 memory. Whenever a new memory technology comes out it tends to have somewhat lower performance than contemporary modules of the previous generation for a while before it shoots up in performance as the technology matures and manufacturers have more time to perfect it.