If you haven't read this, then do so:
http://www2.pgmfi.org/resources/article ... ics_12-02/It's kind of hidden on the site...article by Blundar on exactly what you're asking, a detailed step-by-step how-to on chipping a PM6. After reading just this article I chipped my first ECU, answered all my questions.
The program for a 88-89 ECU is indeed different than that of 90-91, although I'm not sure exactly what changed. Some ECU's have a date marker on the side of them that say "89" but that was the manufacture year...they went into '90 cars, and thus had the external ROM. Easiest way to know for sure is to open the box and look to see if it's there, rather than try to guess about it...there are some oddballs, so it's not a hard and fast rule, but generally ECU's that came from the 90-91 CRX/Civic si had an external ROM, and is therefore easily chippable.
Read that article, and I hope this info helped. -Z
P.S - Search works for me too...