Applying SCEA but ALSO to another university's scholarship program...?

As the title suggests, I’m applying to Yale early but I’m also applying to the Emory Scholars Program. Although I’m technically applying regular to Emory, I still have to submit my entire Emory app by Nov. 15. I just want to make sure that this won’t affect Yale’s decision in any way?

http://apply.emory.edu/apply/scholars.php

So long as you select Regular Decision (RD) for the Emory Scholars Program you will be fine.