If you insist doing an external EXE application, then you can only use AutoCAD COM API, not AutoCAD .NET API.
There are 2 cases you can somehow integrated AutoCAD .NET API code with your EXE solution:
1. Create a bunch of custom commands with Acad .NET API and make sure they are loaded on AutoCAD startup. Then your EXE App, you use COM API's AcadDocument.SendCommand() to call there custom commands;
2. Do your code in AutoCAD .NET API, and expose it to COM, so that your EXE app can call the COP wrapped .NET API code.
I'd would not do either of them, though.
From your description, it looks like the functionalities your solution provide are mostly for an AutoCAD user, who runs AutoCAD (and your application must work with a running AutoCAD session). So, if I am the AutoCAD user, why do I need run a side EXE application to do the work that can be done in AutoCAD easier, faster?
All the tasks you listed can be done in an AutoCAD Add-in developed with AutoCAD .NET APIs, this way, you not only have a more powerful API support (.NET API vs COM API), but also eliminated extra layer of application (the external EXE app).