ATmega328 decoupling caps: are they in right position?
Use the first layout.  There is no need to split the Vcc feeds like that.

Other issues:

The ground connection to each cap is also important, in many cases even more important, than the power connection.  You haven't show that at all.  Getting that right should be your first concern.  There should be a short trace directly back to the nearest ground pin without running across the ground plane.  Since this is a thru hole part (haven't you heard about the 1990s yet?), the ground pin is a good place for the part to connect to the global ground net or plane.

100 nF is skimpy.  Nowadays, there is little reason to go below 1 &micro;F.  100 nF was the common bypass size back in the Pleistocene because of available technology, not because of being optimum.  Today's 1 &micro;F multi-layer ceramic caps are smaller, have less series inductance, and have lower impedance over a wider frequency range than the 100 nF thru hole caps of ancient times.

1206 package is silly.  Why deliberately pick something unusual when the more mainstream 0805 would be at least as good electrically, and cause less space constraints in layout? 0805 is still easy to hand-solder.  0603 is easy too, although handling parts that tiny can be more of a hassle.  0402 can be done by hand, but I'd rather not.