Hi
Have you read this..
http://www.pangolin.com/LD2000/qm2000pinouts.htm
You need to decide if you are using TTL or Analogue.. I presume analogue would be your choice given you are running a QM2000.
Many people use the red connections for a single laser ( see above chart) for pin details.
There is also, I think, from memory, an article on this subject at the Pangolin site.
As you are referring to a BNC connector do you have a Viasho laser ??.
Yes you do use the 25 pin connector.
Remember most laser modulation signals tend to be "unbalanced" (not always but most tend to be) so the "+" signal will be a voltage normally varying from 0 (off) - 5 V (full on) the other side the "-" signal just gets pulled to signal ground.
You should have got a very good booklet with your QM2000 / Net system which explains in full detail.
There is also a very good article by Bill (Pangolin) on how to wire your projector to avoid earthing issues.... well worth a read for you I think. See Pangolin web site or sewarch here..
Yell out if you get stuck.. we all started somewhere..
Cheers

Ray
NZ