Arduino mega2560 bootloader for a clock generator

Somewhat surprised that no-one has answered you on this, and noted your other enquiry regarding the fuses.

Check the manual for the MCU chip. In general, if you use a clock generator instead of a crystal, you simply apply it to the XTAL1 pin and leave XTAL2 open. Most fuse settings (appropriate for an external crystal) will work in this instance, but one in particular may be recommended.