Hi @shanemcmahon,
When you use the When Green Flag is Clicked, you are running the program from within the mBlock environment. It is executing the program by sending the commands over the air if you are connected via WiFi or Bluetooth. If you want to upload the program to the mBot, you will need to use the mBot Program block instead of the When Green Flag is Clicked block to start the program. If you want a program that will work with the remote control, you will need to write one. Be aware that to upload a program to the mBot requires that you connect the mBot with the USB cable. You cannot upload programs over the air.
I wrote a short eBook that discusses programming the mBot with Scratch (mBlock) that can be purchased here. It’s relatively inexpensive but it covers the use of most of the devices on the mBot starting with turning LEDs on and off and ending with a maze solving robot. (For what it’s worth, the proceeds from the book sales go into a fund for kids robotics)
As a general rule, it is a good idea to upgrade the firmware if the mBot is acting up. That will flush out the memory in case something has corrupted it. Resetting the default program will restore the mBot to factory condition. Both of these programs are under the Connect menu item in mBlock.