Is biodiesel in the top layer?

Yes!

Pure methyl linoleate has a density of ~0.884 g/mL, whereas pure glycerol has a density of ~1.261 g/mL.  The glycerol layer will settle at the bottom because it is more dense while the biodiesel layer will settle at the top.  

Using a plastic pipet, transfer the glycerol layer to a test tube or centrifuge tube.