Transparency/Reflection in GIMP

Thought it might be  useful as we go into livery time to have a GIMP thread  or 2 on the go. I've swapped to GIMP from my ancient Photoshop Elements for this season, and although the online help is reasonable, but skill level and aptitude is zero, so a discussion area might help with making progress.

First Question: How do you manage transparency and so reflectiveness for rFactor in GIMP (2.6)?

When I save a s a PNG I get a "PNG plugin doesn't support layers" message and an option to "merge visible" or flatten before saving. Now I guess that's going to squish any layer by layer concept of separate alpha settings. So what's best practice ? Am I limited to one alpha setting so that my working order should be Merge Visible -> Set Alpha -> Save to result in one uniform reflectivity ?