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Mine is a combination of both. Flexible tubes are good for curved connections and is way easier to route wherever you want it to. It's also good if you tend to move things around since it's flexible. Its drawbacks are: They get hard and brittle over time, the clear ones can have algae growth inside, and they can be punctured. Also with flexible tubing you will have to use metal clamps and these can get corroded with salt creep.
PVC is obviously more rigid, more professional, uses almost NO metal clamps that can corrode and you have the choice of slip or threaded. the CON for PVC is that once settled, it's fixed and cannot be moved around.
Whatever you do, make sure you put UNIONS on pumps, valves, etc. for easy maintenance.
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