It is normal to get slower performance with EB, as we push the engine to its limits. There is no loss of performance by having multiple copies of RTW.

As for recommended specs, I don't know. My suggestion is to reduce video options until it runs as desired (particularly unit size for battle performance). If you're at rock bottom there and still can't get satisfactory performance you'll likely need an upgrade.

There are also some other things you can do with a bit of impact, such as disabling some stuff in the preferences.txt, and hiding the character and settlement names by pressing Ctrl-N and Ctrl-T.