Outside of the technical issues which might occur with a lever in the wrong place, there are some other things that you need to be aware of.
The AI drivers drive their trains like tram drivers instead of actual train engineers or drivers. The AI will drive up to the junction, switch the lever then continue. Another issue to be aware of is AI will by default want to take the right-hand track no matter what.
There are ways around these two issues.
To force driver to take specific tracks or routes, you can use direction markers which work like one-way signs. To prevent a driver from taking a track, you place the marker, the yellow marker, with the pointy end facing against the driver's path.
The alternative simple alternative is to use track markers to force AI driven trains to always take a specific track in their schedule. This does allow for a bit more flexibility because this allows the drivers to take any, specified, rather than just a specific one.
And finally for this solution are path-control rules such as auto-path rules, and other path rules which are used to force the AI to take that specific route. These are quite useful in complex junction areas such as station entrances and yard throats. These kinds of rules will hard-code the route that the train takes ahead of time as well as set all the junctions, signal and everything else so there is no question which way the AI driver will go.
For your switching issues, you can use something called the Junction Link. (Kuid2:122381:10003:1). This is not a perfect solution, but what it does is link both junctions along a route together so they work in tandem. These are quite useful for crossovers, but can be used in your situation as well to align both junctions so that the AI will always have a through route without any stopping to flip junctions. This not, as I said, a perfect solution. Other AI drivers do not see the junction as occupied and will flip levers on the occupying consist and cause derailments, but with judicious use and working out the timing between traffic, these can work out well.
Built-in into Trainz is a default junction direction, which this rule overcomes. With the default direction, set when the route and session are built, can be outright annoying because switches will automatically go back to that position once a train has passed. The problem is what is the best "default" direction. It maybe fine in one direction but not the other.
Anyway I hope these tips and others are useful.