When I Use a create table query I need to create relations between two of these tables. Although when I run the query again it says that you cannot delete/overwrite the table as a relationship exists? Is there any other option?

Why do you need to make a table?

I have IIF Statements against another table and would like to post the results into a new table to re-query against those.

You don't need a make table query. You can use the first query in the second query as if it were a table.

Select *
From YourQuery
Where ....;