If you have Websphere installable CD, check for RAD environment. It comes with Eclipse configured to Websphere (they call it as WebSphere Development Studio Client for iSeries). I have been using it with WS 6.0.
Alternatively, if you are using the regular Eclipse (the one that can be downloaded from eclipse site) you can Add servers from Servers tab (Window ->Show View -> Servers).
For clarity, I've added many servers to my eclipse IDE in the past, however there does not appear to be an adapter for WebSphere 6.1 (however there is one available for 6.0). So in essenece I understand that servers can be added to the IDE itself .. but am trying to seek info if adding a WebSphere 6.1 app server in specific is possible.
Regardless thank-you for your help ... wondering if anybody has added WAS 6.1 app server to eclipse project before, and obviously how??