It sounds like you're either using the pre-release NuGet packages or building from source. Either way, you're using code that changes fairly frequently in the develop
branch.
It sounds like you're on the right track though. The Tiled content importer has recently been split out from the main one, so referencing it from the MonoGame Content pipeline is the way to go.
The best way to see how things work is to take a look at the demos. We try to keep those up-to-date with the latest changes.
For example, the demo shows that there's now two DLL's referenced in the Content.mgcb
file.
#-------------------------------- References --------------------------------#
/reference:../../../MonoGame.Extended.Content.Pipeline/bin/MonoGame.Extended.Content.Pipeline.dll
/reference:../../../MonoGame.Extended.Content.Pipeline.Tiled/bin/MonoGame.Extended.Content.Pipeline.Tiled.dll
The exact path to these files will change depending on if you're building from source or referencing the NuGet package but other than that it's straightforward.
It's not really clear from your question what might be wrong exactly, but I hope this answer leads you in the right direction.