Not sure if anybody is still interested in this, but one can indeed define Sobolev spaces (of high enough regularity, so that due to the Sobolev embedding theorem the maps your looking at are at least continuous) of mappings from a (compact) manifold with values in a manifold using a chart approach.
While it is true (and has been mentioned above) that if you can check the $H^s$-property in some charts they will not hold in all charts (as I can always blow up things by composing with suitable diffeomorphisms). However, if one restricts to ''nice families of charts'' then the approach works and one obtains a Banach manifold (Hilbert if you are asking for derivatives in $L^2$). This has been worked out in the paper
Inci, Kappeler, Topalov: On the regularity of the composition ofdiffeomorphisms
Though this was well known for a long time, e.g. see Ebin,Marsden: Groups of Diffeomorphisms and the Motion of an Incompressible Fluid, the new paper is the most complete account on all the technical details (also the point concerning the charts is at least not mentioned in the original Ebin/Marsden paper). Note however, that the results on the manifold structure require your $\Omega$ to be compact (so no chance to choose an open domain in $\mathbb{R}^N$. Otherwise, there is no way this could be a Hilbert or Banach space in any of the usual function space topologies.
I think that similar constructions, at least for the morphisms but not for the manifold structures, may be found in
J. Eichhorn: Global Analysis on Open Manifolds 2007
(where compactness of the source space is relaxed by requiring bounded geometries)