When linking existing components and assemblies (X-REFs) into a new design for re-use at the moment there is no way to change anyting in that linked assembly. It would however be a very nice thing if one would at least have access to some user configurable parameters.
For example if the assemly that is to be re-used is a linear bearin and rail assembly one may want to cheng eht position of the bearing on the rail without having to creat a new version of the assembly, or without breaking the link.
Here is another example in ascreencast.