I have dowloaded a template for after effects and the logo I have imported is coloured and shows in my logo composition correctly. However when I go to the main composition and preview the video, the logo is now all white?
Your render me comp has shy layers and you have not shown us the flow chart, the modified properties of the render comp, or anything else that would give us any idea at all about what is going on in your project.
To start diagnosing the problem reveal all shy layers, press 'uu' to reveal all modified properties of all layers, then start soloing layers or turning off effects until you figure out where the problem lies. To drill through the compositions use the Flow Chart to help you figure out how the template works.
Provide a link to the template so we have some idea of what we are dealing with. If you cannot figure it out embed some screenshots using the toolbar instead of dragging them to the useless Drag and drop here area at the bottom of this form. Maybe we can help you figure it out if we had any clues to how the comp has been set up.
Agree with @Rick Gerard . Much more info is required. Since the original template logo is a PDF, however, my gut feeling tells me that there is continuous rasterization involved and the original creator did not figure in that substituting the layer with a pixel-based artwork would change rendering order, likely making this just another crappy template thrown together by a hack...