When the gear is tall the fulcrum length is greater (the "weight" on the end of the fulcrum is the prop thrust pulling foreward) and the aircraft feels tippy, so some up elevator is going to be required. How close to the CG the wheel axle is also plays a big part in the tippiness also when the airplane is running or landing "tail up" as in a wheel landing or during the take off run when the tail lifts. If the model is generously powered holding up elevator on the TO run is risky and must be done carefully or the model may start to fly before it's ready and stall,OOPS! On a wheel landing the model will tend to want to pitch foreward when the wheels touch as even if they rotate very freely it sort of applies the brakes and will pitch the model fwd and if you apply up elevator to compensate the model may fly again if it wasnt really going slow enough to land. Practicing and perfecting slowing down and three pointing the model will help in all respects as then the tail is down the GC is rocked back behind the axle and we're going slow enough to stay on the ground at that attitude.
As far as using the Vanessa there isnt much to say, support the model and twist the dowel untill it is level (I dont use a lot of nose down, as you said "more chemical in one tray) balanced is self explanitary so if you want more weight on the nose select a further foreward balance point. If the pointer isnt where you want it add weight to the deficient end and re level and check the spot of the point. Repeat as necessary to get the plumb to indicate the desired spot.