Not exporting correctly AE > ME

I have created an animation in Ae and go to render. I get the error message that quicktime doesn't support the file and have then moved over to rendering in Media Encoder. When I do render through Me, the file does not save the way I have made it in the project. i.e. my animation is on a white background, when I go to render it saves it on a blacked out screen, can't see anything properly. I am fairly new to many of these programs, and I have made sure the transperency and compositions are correct on Ae, but still nothing. Does any one have any solutions, please? Thank you.