Homebrew PCBs

Hi all, great group. I'm a relative newbie using Eagle to make two 
sided boards. Have build a cnc machine that will does double duty to 
drill the holes for me and use TT with 10mil tracks with magazine 
paper and even regular hi grade copier paper on a HP IIIP with fair 
success. Tried milling isolation but that's no good for more complex 
or densly packed boards. 
 
Here's my problem I'm doing a lot (for me) of prototype boards with 
db25 connections right angle and 0.100 dual row connectors. What's 
the best way to deal with the problem of through holes for these? 
That is I often find that I end up with a bottom and top track 
meeting at a pin on one of these connectors and I can't solder the 
top connection on all the pins?   

I'm finding that I have to account for that as much as I can routing 
but not always able to, drill over size and wire through before 
fitting the connector or using a lot of via's. I'm presently trying 
to produce  3.5*2." LPT opto isolator with two db25's, 4 9 pin RN's, 
four 16 pin opto's, one 4 pin opt and a bunch of led's and my amatuer 
status is showing and it looks pretty ugly right now......  


Any obvious options that I've missed? the press in through hole 
grommit things and tooling seem to be more than I want to pay. 

thanks..