I wouldn't use a conductive pen anywhere where a simple jumper would work, soldered wire is infinitely more reliable and durable, pens are more appropriate where soldering isn't an option because of heat or because of the materials involved. If it's going to be a long run consider using dabs of non-conductive epoxy to anchor it down so you don't accidentally pull it off later, with some patience everything can be made as reliable and rock-solid as the original traces.
Also either use a Xacto blade to scape off the silk screening to expose the trace's copper for soldering or preferably use a pencil eraser to simply wear it off, it takes come effort but leave the trace in much better shape. Also invest in a decent soldering iron if you don't already have one, not one of those cheapo $10 pieces of excrement that you can pick up anywhere which are like soldering with a heated chip of flint, Weller makes some really good low-budget irons.
I used to work on PCBs as a trade so if you have any questions feel free to PM me.