In my opinion, the best solution is h-towers or similar dedicated tooling designed for each build. However, a quick cheap fix is to make templates to lay in the bottom of the centernest. If you have access to CAD software, you can print out the gerber data or the stencil design file, then sketch in the locations of the pins after a good reliable set-up. Then, go back to your CAD or SolidWorks or whatever you have and draw a template with exact x/y locations. This way you can't loose the templates. You can print it 1:1 before a run, lay it in the bottom of the centernest and place your pins on top of it or punch holes and mark it with a sharpie (marks come off easy with alcohol). If you don't have CAD, use a clear plastic sheet to X mark the spots for pins using the actual PCB/array then keep them for the next go.
(http://www.smtnet.com/Forums/Index.cfm?CFApp=1&Message_ID=66405)