You can have each USRP on the same computer or not,
that shouldn't matter.
I've done this test with some USRP2's and I remember what
we did was transmit a CW tone from one to another and measure
a frequency offset (maybe 10s of kHz?). Basically, transmit a
tone at some known frequency (like 200 MHz) and measure the
received frequency (maybe something like 200.02 MHz) and then
add the 0.02 into you center frequency for this test.
You can also just synchronize the USRPs with a 10MHz
reference and 1PPS.
Devin