Here's my $0.02 FWIW:
1. Not sure what type of filtration you are using. If you are using a HOB, you definitely want the water level to be high enough so the return isn't a waterfall (allowing more CO2 to escape, which you generally don't want in a planted tank), but rather causing a little bit of turbulence at the top (but not too much). If you are using a canister filter, you have more flexibility in setting the water level since you can easily adjust (place) the height/location of the return jet/spray bar. From an aesthetic standpoint, I think a nearly full aquarium is more attractive. But that is my preference and you might disagree (and, of course, you would be wrong -- j/k
). Since your acrylic tank probably doesn't have the black frame/rim at the top, there isn't as distinct a reference point to compare the water level with as compared with the typical glass aquarium.
Keep in mind it will usually be easier to plant your tank before it is completely filled with water. For plants such as Annubias, you can plant them in the tank without much (if any) water. Other plants are much easier to plant if there is some water in the tank (for support). I usually fill a new tank 1/4 to 1/2 with water before planting, depending upon the plants involved.
One other thing about water level: the more water in the aquarium = the more forgiving for when problems/mistakes (i.e., overdosing, overfeeing, heater malfunction, power loss, etc.) occur. But don't overfill the tank such that turbulence generated by the filter causes water to flow out of the top of the aquarium, especially if the light fixture is resting directly on the acrylic top.
2. Assuming the bubbles appeared after you initially filled the tank, it is not an issue -- you want oxygen in the water. The air bubbles will go away as oxygen is gradually dissolved into the water. Under normal circumstances, water contains a given amount of oxygen that varies with termperature. If the amount of oxygen in water has already reached its saturation point, no more O2 can be dissolved into the water until some of it has been consumed/escapes.
3. Sorry, can't help out here as I haven't attempted to repair a scratch on an acrylic tank. Perhaps you can learn from a magician and use misdirection (i.e., a well-placed attractive plant or other item) to divert attention away from the scratch. Unfortunately, acrylic is much more susceptible to scratching than glass. Be sure your cleaning tools are specifically designed for acrylic aquariums. If/when you do clean the tank, make sure you don't catch any substrate (or other objects) in your cleaning tools.