Minecart routes are at heart quite simplistic, they only account for a single cart going through the stops in a fixed order. A cart in an 'out of sequence' location is always considered misplaced and will be re-located _by hand_, even if there's a safe track connection.
I haven't gone far into actual minecart hauling - just stayed with single-lane systems for most actual uses. My attempts at automation were rather unconvincing, even with a single cart - it seems the dwarfs have trouble properly keeping track of multi-stop routes. I used lever-operated doors to 'send' carts from one stop to the next, and the dwarfs decided the cart had no right to be at stop 3 and dragged it back to stop 2.
With multiple loading stations, you'll probably have to make it so the cart will only return to its 'proper' loading bay which cannot be used by other carts (hmmm, distinguish by weight? There aren't very many usable plate settings, unfortunately).
Edit: example for weight-based cart switching into 'associated' loading bays - this requires the carts to be empty when approaching:
.A.A.A.A.A
1R2R3R4R5R--f
.a.b.c.d.e
.|.|.|.|.|
Carts come in from the west, moving east, each 'R'oller sits on top of a SE track corner, pushing west. If a roller is powered, it reverses the cart and pushes it around the corner to the south. There are gear 'A'ssemblies serving each roller.
Pressure plates on the straight track, 1-5, are linked to the gear assemblies powering the rollers immediately east of them. All plates are set to trigger on track vehicles, using the weight settings - first plate for weights over 100kg, second >250, third >300, fourth >350, fifth >400. Originally, all assemblies are engaged and all rollers are active. A wooden minecart won't trigger any plate and is diverted by the very first roller, ending up in branch a. An aluminium minecart will trigger the first plate and turn the first roller off, but fails to trigger the second plate, so the second roller stays active and sends it into branch b. A tin or pewter cart can pass the first two rollers but not the third... a silver cart activates all pressure plates and disengages all gear assemblies, turning all rollers off and landing in branch f.
100 game steps after a cart has passed, the pressure plates reset, engaging the gears again.
I haven't tried this out, but it should work.