What fuse settings for bootloader

I am debugging a self assembled Mega2560. I seem to get sw in, but it does not run I think. I wonder if some fuse settings are needed. Mega16U2 is probably working because I can see a new com port in my pc.

I am using 16MHz crystal.

(deleted)

I see. So burning the bootloader with Arduino IDE helps. I havn't had much success there. I burned then with AVRstudio and did not care about fuses.

Leif