Homebrew PCBs

Hi I've ben reading this group for a while and I feel confident 
enough to make my firt PCB. I decided to use the PnP transfer paper 
and iron it on. Right now I manage to transfer my design to a copper 
bard fairly well. The thing is that I see all those holes and they 
are so smal. I hear some people drill the holes after they etch 
becase they can use the hole as a guide. Well, I tried driling a few 
holes in a practice pice of copper board nd I keep missing the mark. 
The board an't een etch yet but I wondering if I should drill the 
holes fist that way I can add more resist in case I screw up.

   My second question is about sharpie pen. When I was transfering my 
desing a few pads and trces did not transfer properly. I took a 
sharpie pen and fille in the missing gap. Will the sharpie resist 
ferric cloride or will it fail?