If you mean CS-Script as per http://www.csscript.net/, then yes it can reference and call into other assemblies, with the normal syntax:
using MyOtherAssembly;
CS-Script uses implicit loading to try and work out which assembly to load based on the namespace in the using statement. This is not guaranteed to work in all circumstances, in which case you will need to use explicit loading, e.g., you can give CS-Script a directive to explicitly load the required assembly:
//css_ref "..\MyOtherAssembly.dll"
using MyOtherAssembly;
The //css_ref is a special comment that is processed by CS-Script as a directive to load the assembly, in this case the referenced assembly is in the parent directory of the script. This does a similar job as an assembly reference in a project file for a normal assembly. You can also use the CS-Script command line to explicitly load assemblies.
I have also found that you do not need to use either implicit or explicit loading if the referenced assembly has already been loaded into the AppDomain before the script is called. I assume CS-Script detects that the namespace already exists in the AppDomain, so does not bother with the implicit loading.
More information about the assembly loading is given here: http://www.csscript.net/help/using_.net_assemblies.html.
Edit1: You can't disable the implicit loading, but you could put the script into a directory without any other assemblies, which will prevent the implicit loading from being able to find any other assemblies. The script will still be able to call into namespaces that are already loaded. But this is only "security by obscurity"; the very nature of managed code means that it is always possible for a determined person to access your code via reflection.