When you obfuscate your dlls it is possible that you obfuscate public members that become invisible for main exe and other dlls within the same project. Also different dlls can have similar members’ names inside that can be obfuscated differently or have a name conflict.
For this case, RustemSoft suggests to obfuscate your executable by the following scenario:
1. Open a main assembly (usually this is your project main executable) in Skater.
2. By using Linker interface select referenced and non-referenced assemblies and include them.
3. Do not apply any obfuscation settings for the main assembly. All assemblies have to be not obfuscated before. (Uncheck ‘Obfuscate All Private members’ on Options tab too if it is checked)
4. Run obfuscation. Actually the obfuscation will not be implemented since you do not select any obfuscation settings. It will just link assemblies into a single module.
5. Open the linked single module in Skater interface. Apply obfuscation settings to the obtained .NET assemblies' bundle and then run obfuscation.

Skater .NET Obfuscator protects your .NET assembly code against most of known decompilers and modern .NET assembly browsers by applying perfected Control Flow algorithms. These processes harmonize conditional, branching, and iterative constructs that produce valid executable logic, but yield non-deterministic semantic results when decompilation is attempted. Control Flow obfuscation produces spaghetti logic that can be very difficult for a cracker to analyze.
To figure out how Skater does that please try the following scenario:
1. You have Skater evaluation installed. Open Skater.exe (that located in installation folder on your PC) in Reflector or ILSpy interface.
2. Try to browse code within obfuscated classes. Skater is protected by itself and you will not see the C# or VB.NET code decompiled.