My gut tells me that you would want to run the PVC pipe (3/4 or 1" sch 40) to a point at the shore that allows the weighted line (5/8" id) runs to be about the same length (each with a flow control valve). I would actually consider running PEX instead of PVC also.
You do not want to run out to the first diffuser and then "T" off and go to the second. This will not allow for any individual flow control and if one is deeper than the other it will flow less where you may want more. The first diffuser will get the bulk of the flow and the second will get what's left over. AND, if one diffuser blows out, the second will suffer and you can not turn one off for maintenance.
I would also be concerned about using the Pondlyfe system as it is only rated for 2 CFM max. This tells me that you will loose CFM's the longer you make your lines, but I could be wrong...they tout that it is good for depths of 30 feet and their pump may not suffer as much with longer tubing runs like a rotary vane or diaphragm pump would. I'm not privy to their systems and strongly suggest you contact them directly before purchasing and/or designing your line runs.
