Yes You can manage DB from both. But why you are going to use EM instead of Cloud Control 12. You Can do each and every work from it more tan EM. Cloud Control 12c is very good tool.
No. But You can easily setup them using manual agent push or auto discovery method from cloud control 12c. You need to create password less ssh login to both side for oracle user and open the relevant ports from network. It is very easy. After add agent you can add targets from relevant hosts easily.