Muhammad,

there is nothing special in parameter estimation for MIMO systems. If I understand you correctly, you mean correlated states or, in other words, that the states cannot be decoupled. This is the standard case. The fisrt thing to start is to familiarize with the notion of observability:

http://en.wikipedia.org/wiki/Observability

You can also take a look at basics. For instance:

http://www.it.uu.se/edu/course/homepage/systemid/vt11/Sysid2011b.pdf

These lecture notes come along with examples in Matlab.