Breaker panel to transfer switch
Never.  You cannot splice the output of 2 breakers together, EVER.  

North American wiring is done in a "tree" topology, with unlimited branches permitted.  I mention this because most of the time, you see a "vine" topology, and people think that is somehow required.   

What this means for you is that your FORMER 2 circuits can be rearranged to be branches of 1 circuit.  The 1 circuit lands on 1 circuit breaker.  The other breaker then goes unused, leave it in place so you don't have a gaping hole in your panel.  

With this conversion done, the way to work it with your transfer switch becomes obvious.

Since you got a huge transfer gang-switch, and even 10 circuits is not enough for you, I must honestly say you would've been better off going another way: a subpanel.   You get a $130 subpanel, two "main" breakers for $9 each,  a $30-60 interlock kit, and each generatable circuit lands on the subpanel instead of the main using regular breakers in the normal way.  No restrictions on number of 120 vs 240 circuits, and as many circuits as your panel has spaces, minus 4 for the interlock.