Are you going to make the PCBs yourself? If so, you could add the logo with an image editor after export from Eagle.

Here is an example of a logo.

There are many ways to to it.

The most simple way is using the respective layer (bottom, top or tPlace (component)).

The "HJZ" is composed of three single letters being placed the way the logo should look like using a grid size of 0.00625inches.

If your logo is more complicated you should make a separate library, e.g. "LOGO.lbr"

Depending on the qualitity of the design use a very fine grid to create a "package".

Using grid size 0.00625inches and 'grid' on , 'lines' the screen is divided into "pixels" which you fill using 0 trace width and the function "rectangle".

While designing the logo zoom out from time to time too see if edges require smoothing and add another "pixel".

To make the logo invisible on the schematic just don't give it ">NAME" fror the symbol. I'd at least give it ">VALUE" in case you want to delete it. To find it in the schematic I suggest putting it into the doc field at a position easy to remember (e.g. "REV"). As long a the 'component' has no value it remains invisible.

Boncuk