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Yellow coloured packages, do I do anything?



Finally getting to grips with Wyrebash and installing skyrim mods but I do have a quick noob question.  I am installing the packages in STEP order, being careful to name the packages via the naming system but I have noticed that whenever I install a later package that overwrites a package in a lower order, the overwritten package box turns yellow.  Now I have the order right (as per STEP), BOSS is doing its job,  I have the AUTO ANNEAL function enabled, the description of the overwrites appear accurate, but I can never get the boxes to turn green, are they supposed to??  The Wyrebash guide seems to suggest by running ANNEAL the boxes should be corrected to green????  Are the boxes supposed to be yellow on overwritten packages???  Sorry, I am sure this a stupid noob question, but I am determined to get this installed and understand the process.  When I test Skyrim, the mods to all appear to be installed and running, is there something fundamental I have missed?

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