Explanation Of Connecting
It's advisable to have a preliminary idea of the layout before beginning. A rough diagram on a sheet of paper helps.
I mounted the 26-pin stacking (long-pin) GPIO header near one edge of the board, with the female (plug-in) part of the header on the copper-trace side. The trick is for the header not to mount flush against the board, but to stand off about 1/4" high, in order to permit soldering the pins to the copper traces. But, first, we need to cut thirteen rows of traces where the GPIO header will mount so that adjacent header pins will not be shorted to each other (see 2nd and 3rd illustrations).
Cutting the traces requires going back and forth with a sharp knife blade with a fair amount of pressure (caution!), then follow-up checking with a continuity tester. It's a fair amount of work, and next time I try something like this I'll probably use a Dremel tool with cutting disk, rather than a knife. With the thirteen traces cut, carefully mount the GPIO header approximately 1/4" in elevation.
This will give enough room to maneuver the tip of the soldering iron between the pins to solder them. A couple of dabs of poster-mounting putty hold the header in position prior to soldering. Solder one end pin, then carefully straighten out the header so it sits perpendicular to the board. Solder the remaining pins, then use the continuity tester to look for shorts between pins, both sideways and across.
A good continuity tester with an audible indicator is especially helpful here. After soldering, the header pins will protrude 1/4" or a bit more on the perfboard (non-solder) side. This is convenient, as these will function as posts to attach patch-cords and jumpers. Each post will be an electrical connection to the corresponding GPIO pin underneath when the board is mounted on the Pi.
Images Of Connecting