You can not override default order of trays, except if you manually issue PCL6 commands to the printer along with each print job (which I doubt you will manage to code yourself).
Instead, you may get used of built-in functionality:
- you may manually select Manual tray to be the ONLY paper source under "Paper" tab on print properties
- the Automatically selected order to search for SELECTED paper source media is:
Manual Feed in Tray 1
Tray 1 (100-sheet multipurpose tray)
Tray 2 (250-sheet tray)
Tray 3 (500-sheet tray)
Which means, that if you manually insert the CORRECT paper to manual feed Tray1, it will be automatically grabbed and printed on, even through there is some paper in Tray1. If your printer does not behave that way, you must have been set wrong paper size for manual feed Tray1.