For the controlled-not gate, the gate maps input states to output states. Depending on what input you give it, you expect differing outputs. So, yes, there are input states which incorporate all 4 basis states and give a linear combination of all 4 basis states as output. For example, the state
$$
|00\rangle+|01\rangle+|10\rangle+|11\rangle
$$
is mapped to itself. So if you input that state and perform standard measurements on the output, you'll get each answer with 25% probability.
There are also input states which only give you linear combinations of two basis states on output. However, if should be noted that controlled-not preserves the number of basis states involved; it is just a permutation. So to get a linear combination of two states coming out, I need to put in a linear combination of two states. This might not be entangling. For example, $|0\rangle(|0\rangle+|1\rangle)$ does not change. It starts separable and stays separable. Whereas the state $(|0\rangle+|1\rangle)|0\rangle$ becomes $|00\rangle+|11\rangle$, an entangled state. (In both of these cases, you get two different outputs with 50% probability each.)
So, how do we know that a given controlled-not gate is behaving as we think it should be? You need to do some tests in it first. The obvious tests are to start with each of the 4 basis states $|00\rangle, |01\rangle, |10\rangle$ and $|11\rangle$ and see what outputs they give you. Do they match what you're expecting?
Then you want to test the gate in a different basis as well. This might just involve throwing some Hadamards into the initial states. Particularly if you're interested in the entangling properties of the gate, you might check those directly. For instance, if you supply the state $(|0\rangle+|1\rangle)|0\rangle$, we've already said that it should produce an entangled state. So, run something like a CHSH test on it to verify that it's behaving in a genuinely non-classical way (and quantify how much).