We have our site navigation done. When we create a content we tag it with certain tags like images, sales, etc and we also assign it to navigation as to which part of site it should appear. Sometimes the name of the tag collides with the name of the navigation and user gets confused. We also have search on our site. When we have Tag filters and users sometimes feels if he can also have that navigation filters there and sometimes it all just becomes confusing for him. What is the usability suggestion around it.
My understanding is that tags are a flexible way to navigate content. Adding a navigation panel with rigid categorization to achieve the same purpose (content navigation) may complicate the experience, not to mention that it would be redundant.
Your navigation panel, if you choose to keep it, shouldn't conflict at all with tags, not just with keywords but also with purpose.
You've hit on the core concept of Information Architecture design here. You need to have an understanding of what content your site will hold (now, and in the future) and define a set of categorisation techniques that will allow this to be as flexible and intuitive as possible.
I'm kind of with DA01 here - we probably need a wee bit more to advise on the core cause of the conflict, what the conflict actually means and what suggestions we'd offer to resolve it.
I know it's a little simplistic to suggest that all content fits nicely inside one navigation box - it can often not be the case. But maybe your navigation items, if possible, should like "super-categories" for the tags of content they contain? Let me know if that doesn't make sense.
Navigation allows users to find different sections in a site. Each section contains content which is categorically similar. Navigation allows users to find things by navigating to a section and browsing through content.
Tags are descriptive words that describe the content. Tags allow users to find things by searching for specific keywords. It does not matter what category they are in.
In the instance of a word such as 'sales' being used for both navigation and as a tag... If you are unable to make it clear that the word 'sales' is used for both navigation and as a tag using design methods such as proximity and hierarchy, then just make them unique, change one to 'On Sale' or 'Sales Department'.
If you have site statistics which show you what people search for the most, use that as a guide to how your search feature will work. Unless there is a lot of content it might be easier for users to search by tag and without filters.