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How long did it take you guys to learn to operate flaps whilst maintaing pitch?
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That's kind of a tough question to answer, because it really depends on why you're deploying the flaps. If you're trying to simply slow the plane in order to practice slow flight (which is my guess at 3 hours) then you need to know what the plane will do when the flaps come out, which varies by model (for example the C172 wants to go nose high as the flaps come out). That way you can anticipate what will happen and compensate for it with pitch or power inputs.
If on the other hand you're putting the flaps down in order to decend then you'll want the nose to drop, but not too much because if you're flying a traffic pattern you want to use pitch to control your airspeed.
My guess is that you're working on slow flight, in which case you need to keep the plane flying at a steady altitude, but very slow.
As I'm not a CFI I can't offer a professional opinion, but my guess is that your issue is that this is all really new to you, and you do things you're not aware of, because there is so much going on. For example I used to put the plane into a slow left bank while adjusting the trim. I'd get the plane all nicely trimmed up and we'd be flying in a really nice cirle.
It's good to discuss this stuff with your CFI. Remember he knows a heck of a lot more than you do and unless he tells you to buzz his buddy's house at 300 ft, do what he tells you, but he might not be explaining something to you in a way that you understand (everyone learns differently). So maybe ask him to explain it to you another way, or maybe get an explanation from another CFI. You might also ask him to go over how to trim the airplane (if he hasn't already). You might be fighting the plane a bit too much, because it isn't trimmed.
One thing that really helped me in general was to realize that flying an airplane is a lot of trade offs. You can trade altitude for airspeed, power for pitch, etc. For example if you want to climb you raise the nose, which slows the plane down. Inversely if you want to decend you can pitch over and you go faster. If you want to go faster without decending, then you add enough power to hold you altitude as you pitch over. It's physics in action.
Stay with it. It's frustrating as hell sometimes, but remember your CFI was where you are now.
Naunga