I chose to run the lines out of my pump house separately because I wanted to put flow controls on each diffuser line to help equalize each boil and/or shut off each diffuser individually. I plan to use one diffuser in the winter so being able to turn the individuals off is a must and should one need repair, I can shut down that line only. Equalizing the boils is not that important unless your diffusers will be at much different depths in the pond. If one diffuser is at 12 feet and the other is at 2, there will be a significant difference in the amount of air each one receives. The deeper one will be very weak and the shallow one will be boiling like mad.
If there is a very strict budget, running one line from the pump to the water will be a bit of a savings especially if you have to go real far. If you are trenching the cost of some pex tubing and fittings is pretty minimal compared to trenching again.
Here's and example of how I plumbed my pump. The pump is hidden above the plumbing in a fan cooled "box".
