DevinW,
Great questions, I will be sending this to the documentation department.
The second number is the devices or columns to test. Say you have 2 CPU's but only want to test the first one, the PDO entry would be CPU&1,1, to test them both CPU&1,2, to test them all CPU&1,15, PC-Doctor will only attempt to test enumerated devices so 15 will catch them all. To not test any CPU&1,0.
insofar as the DOS logs there is no %systemroot% equivalent but in most cases the boot device will be a: so if you modify the autoexec on the dongle and boot from it pcdr.exe /ba:9 /pr:a:/logs/test1.log /an will get you where you want to go.
-Fred