Yes you can design scripts that help you merge entries and/or delete duplicate data. How you do that will depend on the data you are importing. Sometimes it helps to import into a temporary table and then run scripts that parse your data into various tables from that one temp table. Other times you can even import the line of data into a single text field (it can even be a global field as I learned from LaRetta a while back) and auto-enter fields can parse the data during the import. Other folks find using different software to preprocess the data useful. These are just possible ways to do this you might want to look into. It depends on your data and what you need to do with it.
"why is it that even though I'm using the BPS services edition kit, when I make a new database it doesn't go into the BPS? the overall look and setup is regular filemaker."
Well because filemaker wasn't designed to work that way. New database is Filemaker's command for "create a new, blank database from scratch". If you want to start from a template, you have to select a template from the quick start screen. I don't know if the Business Productivity Solutions kit has some means of appearing in your list of templates but if they don't, then you have to open a copy of the template file and start using/modifying it to do what you want. You can use your operating system to duplicate a filemaker file or choose "save a copy as..." from within filemaker.