I don't think it matters. I don't pay any attention and have never had one clog. I inject fertilizer, but only water-soluble.

The emitters go up.

From the mouths of babes. My 6 year old was helping me run the lines today and he was adamant from the start that the blue dots had to go up. I realized I had no idea, so thats what we went with. System is up and running great now. Thanks.

The reason for facing up is that throughout the season you are bound to get grit in the line and the grit sinks thereby helping the emitters to remain unclogged. There are worse things than facing down- you could twist the line or you could get a hole somewhere along it. If you get a hole it is also best facing up so you can hear the water stream against the plastic and splice it.

Cole, you can block emitters quickly using a complete water soluble fertilizer if you have hard water. Under basic or neutral water pH the phosphorus in fertilizer will form Calcium Phosphate precipitate- Fastest way to block emitters.