Dejan,
The theory behind the Eclipse platform is that this setup should technically work fine. I have never done it myself nor do I know anyone in this forum currently using that setup. I’m fairly sure NitroX provides a demo download and MyEclipse certainly does so I highly suggest you try installing both and using them side by side.
As far as “How” you do that, I imagine you just install both plugins normally against the same Eclipse install, it is smart enough to load up everything. You don’t need to ‘trick’ it by copying one install into another. (NOTE: I don’t know how NitroX installs itself, this is just a guess.)