I have always applied it to the seam.
Note that there are two types of putty tape used by RV builders. One is the regular putty tape and the other is a butyl product. It is stretchy and doesn't put apart like regular putty tape.
The butyl is what is often used behind windows and trim.
Clay WA5NMR - Ex Snowbird - 1 year, Ex Full timer for 11 years - 2004 Winnebago Sightseer 35N Workhorse chassis. Honda Accord toad.