Homebrew PCBs

Hi all. I downloaded the deskpcb software and it seems to do a good 
job. I was wondering if anyone else has given it a spin. If you have, 
here are a few questions that maybe you can help me with. In the 
create g-code section there are a few parameters that I can't figure 
out: Tool # - what are the definitions of these tools? I'm also 
getting an error on that says 6 traces could not be routed. Is this 
because there is something I'm doing wrong with the initial layout, 
or perhaps my trace size? I'm using a 60deg. bit from think & tinker 
and some 2 sided board I got from them as well. As a final question, 
what is the best way to line up the board after you flip it over to 
cut the back side?

Thanx,

Doug