Generally speaking, Permalink Manager replaces all occurrences of the original (old) URL with newly customized ones. This means that meta tags, sitemaps, etc. will use the new URL instead, so Google and other search engines can detect it.
Please bear in mind that, even if the old URL is no longer available and redirected to the new format, search engines may still display the old URL in their search results for a period of time until they have both crawled the old URL and deindexed it, as well as crawled and indexed the new URL. The speed at which this occurs depends on how often Google crawls your website. It may take a few days or a few weeks in more extreme cases.
Finally, if the old URL redirects to the new one (see canonical redirect in Permalink Manager Lite), there will be just one URL listed in the search results.
Thank you and sorry for late response.
So do you mean that if I set new URL with permalink manager plugin it will make it canonical URL and search engine will crawl only the canonical URL and this will avoid duplicate content?