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.