When you "send" code to the robot, you are doing what is called deploying the code from the host to the cRIO. According to the FRC Programming Guide on page 4-16,
http://decibel.ni.com/content/docs/DOC-2631
Deploying the FRC Robot Project
After you develop the FRC robot project you want to run, you must deploy
the program to the CompactRIO device. You can deploy the program in
three ways:
using the Run button;
from the Project Explorer window;
or as a stand-alone, built application.
From your description it's not clear which method you have been using, but regardless of what method you're using, you should still be able to do deploy in any of the three methods to deploy new code. Just follow the directions in the FRC Programming Guide. They talk about it on p. 4-17 (pdf p. 51) and they give a tutorial on p. 5-5 (pdf p 61).
-Nate