Depending on what you're cutting out, you might want to lay it out and mark it on the leather beforehand.

For example, if you're cutting out a wallet that has multiple pieces, it can be a good idea to scope out the grain side of the leather and find a nice area with no major imperfections. Then flip the leather over, copy the pattern using a pen on the flesh side, and cut it out from that.

If you don't want to mark up the leather with a pen, the other option is to cut the pattern out of thin plastic or cardboard and use those edges as a guide for cutting.

Making a stiff pattern/template is especially good if your pattern includes curves.

I've found that it's easier to cut on the grain side, but you can absolutely cut from the flesh side - you just have to be patient and take it slow since it's a rougher cutting area. :)