Do you mean: a. links to the inner pages, or b. doesn't it matter (the idea being that new content --> Googlebots visiting --> will notice the inner pages) if that makes sense ...
Highly unlikely. Google always indexes the index page first - internal pages will follow very soon. It usually takes anywhere from a day to a few weeks, depending on the quality and quantity of your backlinks. It does matter a whole lot but it's always good to mix your links between ones pointing to your main page and ones pointing to your inner pages, simply because it looks more natural (to Google) this way.
So presumably it's always a good idea to vary the pages submitted to directories (ie: mix then up between homepage and inner pages), if the option is there (which, from my limited experience, it rarely ever is)?
just my opinion and experience .. please focus to promote your internal link to social bookmarker or article directory ..many of us only promote the main link so google will crawl main page first.. u can found all of this thru google webmaster .. hope help.