Homebrew PCBs

I have been designing and building a few boards using Staples Photo 
paper (iron on patterns) and I am doing my own etching.

I have been trying to design my boards as single sided boards to avoid 
the problem of getting solder to flow from one side of the board to the 
other in double sided boards.  However, single sided boards pose a 
severe design limitation.

What is the best (read most fool proof) way for a neophyte PCB builder 
to get continuity through the holes on a double sided board?

Thanks,

Paul