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At this point you could use a tool like Binaryen's wasm-merge. It essentially resolves the imports of one module to the exports of another. In case plain merging doesn't work, for example because two memory managers get into each other's way, something similar can be achieved by simply using two wasm files, providing the exports of the first as the imports of the second.
There'll be additional choices in the future, for example once DynamicLinking matures. There's also the pending idea to use a module compiled using another toolchain as the "base image" of an AssemblyScript module, basically appending AS-generated code to the base module while using a .d.ts to describe the functionality provided by it (not yet implemented, though, but shouldn't be too hard to get this going).
I want to use this to link it against a C program, is there a way to do this so a function in my C code can be called from the WASM ?
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