Hi Tim,
You can change the tied notes to "cleaner" notation by (1) clicking on just the tie and (2) clicking the "Collapse ties" button in the tie palette. You can
check out this post for a downloadable video on doing that operation en masse (eg. for an entire score at once).
Mark has improved this behavior to not automatically change eg. a dotted quarter note into a quarter note tied to an eighth note for the upcoming 2.6 release, which you'll get free
ttfn,
Sherry