Hi Ed,
First of all, what you need to do depends on what version of Moodle you use. I assume 1.4.x. Second, you will need to do a little customized programming to achieve the desired effect.
Every course in Moodle corresponds to one record in table mdl_course in the
database. This table contains a "blockinfo" field which holds the information about the blocks in each course.
The blockinfo field in general has the format A,B,...,C:X,Y,...,Z where A, B, C, X, Y, Z etc are numbers which correspond to block ids from the mdl_block table (you can see in that table which number corresponds to which block). The double colon separates left:right blocks. If a number is negative, e.g. -3, this means that in that position we have the block with id = 3 but it is hidden.
Now what you need to do is write a small script that loops over all the records in mdl_course, takes the blockinfo field, does a little string manipulation in order to insert your new block ids in the required place, and then calls update_record or something equivalent to write the data back to the db.
I hope this helps to get you started!