[Paul Jones] “Errr, not sure, don’t have great knowledge on alpha channels etc”
You need to. Google it.
JPEG does not support alpha channels, and even if the JPEG has no background at all besides for the logo, FCP is probably going to do something weird to the edges.
Do a little research. Then bring your logo into photoshop or whatever, make a .tif or .targa with alpha and bring back into FCP.
If it has a white or back background you could pull a luma key but really you should educate yourself on alpha channels first.
Best,
Joey