Yes they certainly will cope with permanent magnets. You can enter the magnet characteristic with all the electromagnetic finite element packages, and in your model you define the direction of magnetization, it's pretty simple.
I have used the free download version of Maxwell (Ansoft), it does the basic 2-D business and it is easy to use (field patterns etc) but I did find it lacking when it came to force calculation i.e very sensitive to the mesh and generally not reliable. The full FE packages usually offer different force calculation methods (Maxwell's stress and the virtual work methods to name two) and generally are a lot better equipped. Calculation of force by two different methods also gives reassurance, it is a calculation prone to error.
The commercial packages I have used are Ansys, Algor and MagNet (the latter several years ago) - Ansys is a bit of a sledgehammer to crack a nut, Algor is quite laborious to model and mesh I thought. MagNet may be the one to go for, I have a feeling it is cheaper, and also has adaptive meshing and a macro function - both very desirable in my opinion.
You may want to ask for a free-trial, I know this is done quite often, but bear in mind there is usually a big learning curve particularly when adaptive meshing isn't available.