You can run the program in memory without deploying it to flash.
Sorry if the exact dialogues are incorrect, but I don't have it in front of me. I'll clarify with screenshots in the morning if desired
You can either Run or Debug Kernel Task directly, after building your project. The first time you do it, it will bring up a Run dialog, where you will be able to configure how your program is run. You need to type in the entry point of the program, which is FRC_UserProgram_StartupLibraryInit for WPILib code. If running normally, just hit the "Run" button, which will start running the code.
If you need to test another build, you must first unload your program from the cRIO's memory - find YourProjectName.out in the Remote Systems list, and delete it (don't change any of the check boxes that come up - just hit OK). Then you can run another version of your code . It's a pain, but it works.
Note that you must also "undeploy" any code you've deployed to flash, otherwise directly running your program won't work.