Yes. You can create as many copies of vanilla as you prefer to install various mods. Personally I have 7 RTW installations:
* BI 1.4 - for copying in case I find a mod I want to try
* BI 1.6 - for copying in case I find a mod I want to try
* EB 1.1 - of course
* EB1 internal version
* FATW 2.5 - recommended
* RTW Vanilla 1.2 - for copying in case I find a mod I want to try
* RTW Vanilla 1.5 - for copying in case I find a mod I want to try
Edit: Actually, it is recommended to install EB into a copy of a clean 1.5 RTW, just as you propose. That way you won't have to install any vanilla stuff if you screw something up and need to reinstall.
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