That is a great question. As far as I know the red elderberry (Sambucus racemosa) and black elderberry (Sambucus nigra or S.canadensis) will not cross pollinate/hybridize naturally, but I think that is mainly due to their differing flowering times.
In most locations they flower around 1 month apart, the S. racemosa has already set fruit as the S. nigra just begins to flower. So by that, I would say you are safe to have them near to each other in your garden.
I hope that is of some help, and that you have a great time growing your elder patch!