Publishing figures without embedding them?
Send separate files in one of the required formats to the system/editor along with your manuscript. Send one file per figure, I would suppose. The copy/layout editor will place them in your final document after possibly some processing. The problem is that the flow of the published document may not match the flow of your manuscript if it isn't just a simple photo reproduction. They are looking for something of higher quality. You should properly label your files so that they can be placed in the correct order, etc. Captions on the figures may need to be handled separately as well, but you should get instructions on that. 

Within the manuscript, don't refer to figures as "the following figure" or similar, but with a proper reference - which will depend on the publisher. Something like "Figure 3.2" perhaps.