Sensing IR using multiple Phototransistors (4 one in each direction)

I'm making an autonomous Blimp that would move to an IR Beacon that we made using IR LEDs. My problem is that when I connect 4 IR Phototransistors that Arduino doesn't correctly sense which phototransistor is getting the radiation from the beacon. I was thinking of emmitting the beacon in a flashing sense for a certain period thus my arduino would understand the sequence but I'm not exactly sure how to do it. I'm not using the IR Library because I'm not using a remote control just a beacon made from IR LEDs.

IR light is all around us, so your sensors could be picking this up. In order to detect a specific signal, you can transmit the signal on/off at a known frequency. You would then look for this frequency in your IR input on the blimp. You may need to resolve how you would discriminate between a direct and a signal reflected from nearby objects and flat surfaces.

Would you mind guiding me how to find the IR frequency using my arduino? Or would I just make a bandpass filter?

IR Remote systems use a variety of frequencies. Transmitting at that frequency is a matter of pulsing an IR LED at the desired rate. IR demodulator/receivers are able to detect the pulses and output a 1 if the modulation (ie frequency) is present and a 0 if not. IR libraries then decode the bit stream into messages, but you don't need that, as you have said.

I would look at the IR demodulator/receivers, find one you want to use, and then write the sending end to suit.