Are they cutting it on seperate fabric pieces?

Pattern layouts are usually laid out to use the smallest amount of fabric possible. If the pieces are symectrical it will make no difference which side of the pattern is up when you cut them out. If the back is on the fold and the two fronts are alike then you are OK. A more experienced sewer might not choose to use the recommended layout, but if you are new to sewing then it is the safest way. Sewing them together will not be different.

Not sure why they print it the way they do sometimes (possibly has to do with grain and/or continuation of the grain from front to back?), but you are just pinning the pattern to the fabric with the pattern piece printed side down.
You are still cutting all the fabric the same way just as you will still be placing right sides together to sew.
HTH
Cathy

thanks for the info, I feel much more assured now.

I made a skirt in home ec class about 5 years ago, we never got into details of "why" things are done a certain way.

Thanks again.