I'm having trouble figuring out how to build the best TP. The optimizer suggests where to use FP+ but does not tell you which 3 attractions to use them on and it doesn't account for the ability to obtain additional FPs after the first 3. Some have suggested optimizing, then plugging in FP+ in the spots with the longest wait times and re-optimizing, but when I try to do that, it doesn't always use all 3 FPs. I can't imagine that a TP that doesn't use all 3 FPs would be optimal.
If you add more things to your TP, you'll find that the system will be more likely to use your FPs and make more suggestions. Sometimes it doesn't use your FP because it can fit that particular attraction into the plan earlier in the day with a shorter wait time. During the busiest times, even the FP line can take more time than the standby line would have earlier in the day. If you have lots of items in your plan and stay through the busy times, then it will start to use them.
If you plan to get there at park opening, the optimal TP will do a bunch of things back to back without using FP for the first hour or two. Then it will move things with shorter wait times into the busiest hours to optimize your time. It will also make suggestions for good FP options.
But really, you can just get the FPs that make sense to you and choose the "force plan to use my FPs" option. It might be a couple of minutes more waiting time than going 100% with an optimized TP, but the reality is that you get the FPs that are available and use them. You could also do an attraction twice - once in the slow time using standby and then again with your FP.
I made a post with a method for optimizing with FPP and other TP tips - check it out at http://forum.touringplans.com/t/making-optimized-personalized-touring-plans-with-fastpass/1570/
If you get secondary fastpasses in the park, you are gonna find out how cool it is to be able to re-optimize your remaining steps in just a few seconds on the fly after you plug in your new fastpass.