Make sure each kit is in the same color slots.
In BIOS, input DRAM frequency, timings, and voltage.
For timings, tRFC should be increased to 80.
For Voltage, set MCH Core Voltage to 1.40V. This will help the memory controller stabilize full slots of DDR2-1066
If you have problems, try DDR2-800 4-4-4-12 2.0V.
These are fail proof settings you can use to determine whether the two types of kits can be compatible in the same computer.