Homebrew PCBs

Couple of things to try...

Try different angles.  I use another PCB as the squeegee, and I have to 
lean it over more to keep the solder bead down near the stencil.

Mix your paste before using.  It needs to be creamy enough to "roll" as 
you pull the squeegee.  You might need to put more paste down to get 
this rolling action, then return the extra to the tub.

You can practice on an unetched pcb with no stencil; then it's easy 
enough to collect the paste and start again.  Once you get the rolling 
action down pat, try the real pcb.