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.
Yeah Tinkercad is pretty basic, I think there is a why to draw shapes but it looks complicated to me so I didn't look to far into it.
I use mostly $olidworks (there's a student version which you use to be able to get for free if you are a veteran or belong to certain other groups.) but take a look at Onshape (it's just like Solidworks) and basic usage is free (if you don't mind sharing your files that is) it's also web based so you can use it from anywhere without installing anything.
Another good free CAD program is Fusion360, (also free) I've heard great things about it but haven't tried it myself yet.
You can't edit stl files in most CAD programs though (which is the only good thing about Tinkercad) but I will upload a blank version of the stencil in step format (soon) which you can at least cut new shapes out of in most programs.