I used the program called AnyRail when I made my shelf layout. Think you can add up to 20? pieces of track on free version before it barks at you. Has all the different manufacturers track lists. Haven't heard of the one you mentioned. I just used the program again to determine what looked and worked the best to add a few turnouts for Thomas to stay in his room. I picked up Lionel's Thomas the tank engine along with Annie and Clarabelle cars, though in O gauge. I want to get the rest of the gang, but they are all sold out.
Years ago I had an HO layout. In one spot my dad installed a Peco curved radius turnout. For some reason, the cars like to derail over this one switch. Also as your talking about doing layers, make sure Thomas can climb those gradients. Would hate to build it, only to tear it down and redo or keep giving Thomas an extra push in a few spots. Then as your doing flex track, and I guess your going to solder the connections, its easier to solder them with track being straight, then making the radius you want. That way there are no kinks at the connection points of track and eliminate the possibly derailments.
I was a kid and had the up and over figure 8 layout. I ran my engine full speed all the time. I am sure Thomas will have some speed runs. Just make sure trackwork is smooth as possible and kink free at the joints.
I looked up what radius Thomas can run at. Says 15" radius or greater. I know with program I used, I could set the minimal radius. So if I went beyond my setpoint, it would turn red. I also have a HO shelf layout in one room. I ordered some "sweep sticks" from hand laid track . com. Laser cut hardwood pieces that go within the rails to help keep a consistent radius. I too used Atlas code 100 flex track.
Go with a bigger radius on your layout plan, Thomas will be happy and you can add other trains down the road.
This is my Son's room. Thomas up top on a side track. Can run my other trains around the house, and keep Thomas in his room. Then underneath is an HO shelf layout. Uses the 2% foam gradient from woodlands scenics. Will be a 2nd track running at the base eventually. Working on turning the foam gradient into a hill and rock face.