Yes this is the most difficult part, making sure you don't take the donor
colony's queen by mistake!  I usually look for her, and once found, set her
comb in a nuc box until I am done taking the brood and bees I want for a
split.
 
This is, admittedly, time-consuming and tricky.  Eventually you get to the
point where you are just looking at the combs you pull to ascertain the
ABSENCE of the queen on them. A quick double check and you can be fairly
certain you don't accidently take her away.
 
I wish there were some way to "mark" the queen so that you could find her
location in the hive quickly with a sensing device.  Oh well, maybe
someday. Radioactive tagging or something!  :-)                Later...
JWG