Just started experimenting with Marmoset Toolbag and had issues with baking out the normals, where there were visible seams. After a bit of researching I found out a few tips which worked for me, so they might work for you too.
The guide is on my blog
http://www.vfxforge.com/blog/zbrush-to-marmoset-toolbag-baking-normals/#more-2430
Or you can download the PDF guide here
http://www.vfxforge.com/wp-content/uploads/2014/02/zbrush_marmo_baking_johnchen.pdf
Cheers
John