Practice your squats, keeping your back straight and head up. Repeat until you die :)
I think your instructor is reminding you to 'bend your knees' and not 'bend your back' when lift or need to get low. A common call at many dojo's I'm sure!
If you're tall (I'm 6 foot and skinny) you will find it difficult to "lift" an opponent with, let's say "a low centre of gravity" but it can be done. The good news is when you get it right, it's a lonnngggg way down for uke!
Concentrate on improving your strength and flexibility in your ankles, knees and back. Don't worry too much about achieving the perfect "throw" (i.e. up and over via the hip) - it might be a bit messy (i.e. the uke slips off your hip or falls around your legs) but with practice, technique and timing you'll find the "sweet spot".
Be realistic, if you can develop a strong low squat and take their balance (by getting your CoG below their's), then they will be thrown.