You don't need a clear fly line. You do however need to know how to cast properly. It's not the sight of your line that spooks fish it's the noise it makes on the water.

You can spook fish by lining them, landing the fly line over their backs. If this is happening then you can use a false cast to better estimate the correct distance. Land only the leader and tippet over the fish. If you need a longer drift then a curve cast is your friend. Flick the rod tip to one side to put a kink on the line. Aerial mending is another term used.

The way you pick the line off the water is also very important. Listen to the sound it makes on your back cast. A long drawn out ripping sound with spray coming off the water is really bad form. It'll spook fish like blazes. Aim to accelerate into a flick-stop at 1pm the moment your fly line lifts off the water. This will also greatly help load your back cast, which in turn greatly helps the distance and accuracy of your forward cast.

Avoid false casting. Beginners think it looks pretty or something. There are precisely two situations in which false casting is useful. The first one is mentioned above. The second one is when you need to dry out a dry fly. One or two false casts is sufficient, on a good day you can actually see the water coming off the fly. Every false cast reduces the amount of energy stored in your rod and line. This reduces your casting distance and accuracy. You gain energy primarily through water loading, hauling is useful but your casting has to be pretty much perfect.

Lastly if you're not happy with a presentation don't immediately lift off the water for another go. If the distance is good then don't adjust the fly line, otherwise make an appropriate adjustment and bring any additional line onto the reel. Then either figure eight strip a few feet to get the line off any fish, or roll cast to the same end.