nonmanifold geometry sometimes appears if you mirror wrong. subd especially does not like to have a useless vertice (like one that is only connected to 2 edges in poly proxy mode. as for the seam - there is an relatively easy solution to it:
the tangets at the edge needs to be flat at the seam. instead of modeling exactly one half, model more than one half. create a half, and extrude the edges in the middle exactly to the other side. now if your half of the model looks good with the extra faces you can delete them, mirror geometry (i suggest you do that in poly mode) and merge afterwards the verts. it should be nice and seamless if you merged the verts and if you had all the verts exactly in the middle. easy way to put them in the middle is to select them, move and grid snap along e.g. x-axis - and then move back there they bolong to.
hope that helps some - and of course there is always other methods to do it ...