If there are any MWBCs connected to the three phase panel downstream of the transfer switch you will not be able to simply parallel all three lines to the generator output.
If the generator output is 120/240 single phase and your service is 208Y/120 it gets more complicated, since it will be harder to balance loads to the two sides of the generator.
Really single phase, as in only one ungrounded bus? Or "single phase" as in two out of three phases brought to two ungrounded buses?The main panel is 3 phase but all the branch circuits are fed from 100 amp 1 phase panels. My plan was to make one of the sub panels into a generator panel with an ATS between the main panel and sub panel.