FireWorks’ Stroke feature gives the user three basic options: align to outside, align to center and align to inside. On top of that you can use Photoshop Live Effects Stroke with those same basic options. With simple rectangular shapes there is no visible difference but not all of them rendered equally elegant results when used on rectangular shapes with rounded corners.
Here is a small table that shows the difference:
As you can see, the best results were produced with FireWorks native stroke aligned to outside and stroke aligned inside or outside with PhotoShop Live Effects. Neither seemed to handle align to center well and that's because the only way to nicely render center-aligned stroke is to use Fill Over Stroke option under Stroke Options:
Utilizing this option, you can render nicely rounded corners with center aligned stroke set to 2 pixels (where one pixel is covered by the fill)
With this simple adjustment, you can have elegant results no matter the alignment.