This is the very same point I'm at with the system I'm using. I'm absolutely confident in the systems ability to create great entry points but knowing how far to let the profits run is always difficult. I'd suggest doing a statistical study of your own past trades using the system. You're very likely to find some common areas of resistance (or support if shorting) that tend to hold in your unique situation which you can use to take partials/exit. When you know the probability of your winners running to 2R, 3R etc versus the win/loss ratio (obviously this will become smaller as you increase the R value) you can then decide whether you're comfortable letting them run further (if the statistics suggest it's a good idea)

I can get a fairly good idea of a stocks range of movement (as a percentage), based on looking at a chart. For longer term swing trades, I set my targets as a percent from my entry point. I would only take profits if it broke my trailing stop (from some set moving average, not the price) before reaching the profit target.

For day trades, my method is different. I work off of pivot points to find an entry point. I am now familiar enough with the stocks I day trade to know how far the price usually will run from the pivot point. I only day trade stocks that I have watched and have an understanding of their typical behavior.

http://acekingtrader.blogspot.com

http://www.pivotpointcalculator.com