I am having no problems...Thats the problem.
 

I keep hearing about how people need to trans code their footage for fcp, yet i just dragged and dropped the .mov files into fcp and I have no issues with playback. My question is, am I going to run into issues down the road as I am only one minute into my five minute short?

5dmarkii
24fps
1920x1080

System:
Brand new imac quad core 16gb ram 27in i7

Try playing them at a higher percentage of scale. In other words is your canvas window set up to view at 50% or less?

You'll see the hit immediately when you drop a filter on the footage- even something as simple as a 3-way CC.

Just try the difference between scrubbing along the timeline with native files or the same video converted to ProRes. Sure you can do it with native files but it's sort of sticky & jerky compared to using ProRes when it is as smooth as butter.