Which version of the LS6? Gen III small block or 454 big block?
Since you're asking about the complexity, I'm assuming you mean the Gen III small block that was in the C5 Corvettes and CTS-V.
The TH350 can be used, but attention needs to be paid to the flexplate and/or converter. There are a variety of routes that can be taken; modified LSx flexplate with spacer & TH350 converter (couple of routes this way), LSx flexplate with aftermarket LSx to TH350 converter, aftermarket LSx to TH350 flexplate. You'll also need to figure out a bracket for the kick-down.
Mounting the engine in the subframe can also be done a variety of ways.
Sites like LS1Tech.com have all the information (with P/Ns) you need to do this kind of combination. Also check the LSx section of this site.
'66 Hardtop - LSx/TKO swap in perpetual process
'67 SS - Pro-street & forever in pieces