Can taxonomy terms be related to one field only

I am fairly new to taxonomy so I may have overlooked something obvious.

I am using content taxonomy to in a content type created via cck. There are a couple of questions in content type that use content taxonomy and allow freetagging.

The problem is that the fields are not related. However, the autocomplete feature seems to pull from the tags used in both fields. Also when I attempt to create a view and use a filter on taxonomy terms, I need to set up filters only on the terms for each individual field. Currently it seems to pull all the terms from both fields.

As an example one field has been used to store the terms 1, 2, 3 and the other field has been used to store the terms red, blue, green. I need to be able to set up a view filter that will allow users to search on 1 or 2 or 3 (automatically populate with any numbers added via this field). I don't want the filter to include the terms red, blue, green with the numbers.

Is there a way to have the terms stored separately or the associate the terms with a particular field and not with all of the content taxonomy fields?

Thanks for any suggestions.