Sonos placement on a large living room

If you want Dolby Atmos via Arc Ultra and Surrounds for complete immersion you have to go with the first option. I assume the 3rd Era 300 to the right (when facing the TV) is a stand alone speaker as the Arc Ultra only supports two surrounds. 
 

The second option with in-ceiling speakers will only allow Dolby Atmos effects from the Arc Ultra.

First of all, thanks for the help.

Yes, the third era would be standalone (not part of the surround group) but would often be grouped together when playing music. 

I generally also like option one better. Im just scared the table to the right of the tv might not be filled with sound when listening to music

For the top of the room, nothing wrong with adding an Era-100 or two by the worrisome table. 

I'd lean to adding one in each of the top corners of the room myself. Try stand-alone or stereo Paired to see which sound you prefer. I might even swap the lone 300 for another 100 and group the three. 

If the low end feels weak at the top of that big room a mini-Sub or full Sub would help. Tuck it in where the lone 300 sits or for more impact, particularly if using the mini, put it in the top right corner.

For the Arc set you seem to have power by the central couch, a full Sub slid under that would do wonders. At the Arc location would work too. 

Maybe just buy one full Sub and try it both places and decide if a second is something you want.

To fill out the space for music you might consider a stereo pair of Five’s against the North wall reference the top diagram. There may be occasions when you want to enjoy the best stereo Sonos can provide sans the Arc and surrounds. I have a dedicated pair of Five’s in the room with my Arc Ultra and Era 300 surrounds.