I think this will answer your question, but I can manipulate a bit if need be to get more specific.
What you are describing is where exacttarget gets kind of fun, and really lets you open up how you do things. In your template, you probably have added <custom type="content" name="one">
to create content areas in your email. Depending on how you want to set this up, you can add your AMP script to do your propensity score scripting either right in the template (if this is the only email you will use this template with) or as another content area in the email.
AMP script will not be rendered in the email directly, so if you are running through your amp script to make some decisions, just add it to the top of your email, and drop in a content area. The AMP script variables will pass through the entire email to other content areas, so you will be all set.
Then, in each content area of your template (top to bottom), you would add the code like this:
Content Area For AMP script
%%[SOME AMP SCRIPT TO MAKE DECISIONS WITH VARIABLES THAT ARE SET FOR REST OF EMAIL]%%
Content Area 1
%%=ContentAreaByName(Concat("my contents\newsletter\", @position1))=%%
Content Area 2
%%=ContentAreaByName(Concat("my contents\newsletter\", @position2))=%%
Content Area 3
%%=ContentAreaByName(Concat("my contents\newsletter\", @position3))=%%
Content Area 4
%%=ContentAreaByName(Concat("my contents\newsletter\", @position4))=%%
Content Area 5
%%=ContentAreaByName(Concat("my contents\newsletter\", @position5))=%%
It might also be good for you to consider turning on send logging if you can, and capture the send information regarding what content area each subscriber gets where - would be something to consider.
I hope this helps you - let me know in comments if you still are missing something, and we can work on getting it figured out.