When dealing with audio you have to maintain impedance values. An l-pad reduces the voltage while maintaining the impedance.
Now, the square wave being generated has an unknown impedance (if impedance is even a valid term when discussing a square wave). In any case, it won't match the impedance of the input of your sound card.
An audio engineer would insist that you must wave-shape and condition that square wave into a signal acceptible by the sound input. In reality, we're talking about very low-fidelity signals in the first place, so distortion is not an issue. The point is that you must reduce the amount of current being delivered to the input to prevent overloading and possible component frying.
An l-pad might work, a simple resistor in series might also be fine. I would try a 10k potentiometer (10-turn preferably) and you could adjust down from max until the signal is about as loud as your other sources.
I haven't done any audio design work in ages and ages, hopefully I haven't grossly oversimplified...
"We must fall back upon the old axiom that when all other contingencies fail, whatever remains, however improbable, must be the truth." - Sherlock Holmes