How to controle the "Available Columns" list in BOM line in Stucture Manager Module? - Right click on any column name and you get options to insert/remove column. I hope this is what you are looking for.
How to apply a custom preference to a particular user? - Create new preference with "Protection Scope=User". Then in Edit-Options dialog, select "Organisation" (at bottom of dialog). Select the preference. Then select the inteded user from organisation. On top left of the dialog option "Create a new preference instance" is now active (was greyed out till now) Now you will have a copy of preference with "Location=User"