Check the following settings before uploading your firmware:

Tools → Board → Sanguino

Tools → Processor → ATmega1284 or ATmega1284P (16 MHz) (this should be the second from the bottom)

Tools → Port → Whichever COM port shows up

Tools → Programmer → Arduino as ISP

You're now ready to upload Marlin! Click the upload button.

If all goes well, you should see the MakerLab logo on the boot screen of the printer. If it instead says "3D Printer," something went wrong with updating the bootloader. If it's still blank, then you didn't upload Marlin properly.

Make sure that all instances of Simplify3D are closed before flashing firmware to the CR-10. Simplify3D will deny Arduino access to the COM port and it won't be able to communicate with the printer