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I have two fields with percentages. I would like to say that if either Field 1 or Field 2 is not equal to 100, delete (filter,disappear) the row. I would like to do this specifically in the formula tool.(I've already done it using filter module).
You can't delete (or make disappear) a data record using the Formula tool...the Filter tool is the proper tool for doing this.
Now if you mean you would like to create a "flag" field that you can use in a subsequent Filter process (e.g., Y or N), then you would do that in a Formula tool (with basically the same logic you likely already have in your existing Filter tool).