InRoads (Im guessing) uses strings to defign the vertical alignments & generate surfaces.The same can be achieved by just creating assemblies with named points & generic links added then assign these to each baseline. In the corridor surfaces tab yopu then just use the featurelines as the definition but this is more difficult than it needs to be.
With Civil3d these strings are created by the subassembly but the logic is different so you need to work "Inside out" in some areas.
In the case of a junction I normally create an assembly wth ConditionalHorizontal subassemblies added to either side with the pavement added. These will be used as new baselines & regions controlled from the junction kerb return alignments targeting the side road channel line & proposed Centreline. This means that you need either alignments with profiles for the centreline & both kerb returns or 3dpolylines or Featurelines.
You therefore need to build the subassembly from the Channel line outwards, so you could then have on the left side of the conditional subassembly a kerb & footway with Daylight and on the right the road subassembly. For this reason I reconmend using the Generic Pavement as you have the ability to change the codes accordingly (as you want the channel code on the inside and the crown on the outside of the generic pavement)
I guess yours secondary alignment is connecting badly with main alignment. Try it to join with Perpendicular
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