Here is a very simple guide that will show you how the enable the use of your transport controls with your MIDI controller in Fruity Loops 11. For this demonstration we are using the MPK 88 by Akai Professional.
After launching the software click on the options tab in the upper left hand corner.
Select the MIDI tab. You should see your MIDI controller listed. Click on your controller so it's highlighted.
Now Enable Send Master Sync and Controller Type. In the drop down menu, select which brand controller you have. If your MIDI controller is not listed select Generic Controller.
Now you're all set and ready to go!