In general, you always want to keep auto-negotiation turned on, unless the equipment on the other end is specifically set to a fixed speed.
If you turn auto-negotiation off on one end, and the other end has auto-negotiation turned on, the link may fall back to a slower speed, even perhaps as slow as 10 Mbit/s half duplex!
This is because the other side won't see any auto-negotiation, and therefore will fall back to a safe speed.
Even worse, using manual setup you can set up different settings on each end, leading to a link which will operate poorly or not at all.
The other end in this context will be the Ethernet switch you're hooked up to.
Short answer: If in doubt, turn auto-negotiation on, and don't manually try to force anything. You'll just create more problems for yourself if you do.