I'm unsure exactly which users would want to implement your commenting system into their blog considering a lot of people will just use wordpress, or another popular blogging platform - or if they have developed their own, I would have thought them 'savvy' enough to also implement their own system.
Anyway, onto your question:
You cannot force comments entered through your system to receive any 'special attention' from search engines. It's very much down to the content users create as actual comments. If users post comments like "Nice post" or "Good work", they probably aren't (and shouldn't) be included in SERPs (search engine results pages). If somebody posts something insightful, it might be included - but if we're assuming it will follow standard blog commenting practise - i.e. they're situated below the blog post, the content within them will not have as much of an 'effect' on what results the entire page appears for.
On the other hand, if you had an extremely popular/valuable blog post, comments would more likely be crawled and indexed along with the entire page.
Basically - You can't force comments to rank, it's purely down to the value of the page they're situated on and the value of the comment itself. When I refer to value, I mean whether SE's think it's valuable.