MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
One of the "pins" files (there're different ones because of errors in printers) should stick through the stem through the sepals to the bottom of the rose. The pin is hidden so can be any color. I'm guessing you didn't notice that file.
If you printed the thorns separately, then you'll probably need to glue them to the stem with an appropriate adhesive for your filament material. They might press-fit, but I'm not sure they'd stay very well. (I didn't test that very much because I have a 2 extruder printer so I just printed them all together.)