Register your .in domain with Google webmaster tools, and there is a section there to geotarget India. The thing is, it shouldn't be necessary because Google has already expressed that country-specific domains such as .in are already targeted to their individual countries. But it can't hurt.
It might also help to cross-link between your two sites, if you're not doing that already. I suppose that each domain would need its own individual set of backlinks, as well.
yes you can target geographically.Also you should try to submit your business in Google local listing and local Indian search engines or directories. If you ll try this method you ll really get your website in .in too.
If you are trying to Target any GEO, then make sure that you build enough backlinks from that particular GEO. For getting more local backlinks search for directory, local search engines, local web sites for link exchange and so on.