I'm curious as to what you did to get yourself lower. Generally most people will simply lower the bars. If you've set up your seat position so that your legs and torso are properly positioned previously then you shouldn't really fuss with that too much. If you lowered your bars then you might have to play with saddle tilt a little bit or it might be that you just need to give yourself some time. Try going back to the original bar height and lowering it incrementally to give your body time to develop comfort with the new lowered position. You can do this by playing with the spacer stacking. Hopefully you haven't already cut down your steerer. Move some spacers from the bottom of the stem to the top to gradually get it lower. Lower it only 5mm at a time. If you can't "tune" with enough granularity using the spacers you already have, you may need to purchase a new spacer kit with more smaller spacers. Keep in mind too that as you lower your bars, you not only increase your reach to them because the perpendicular distance increases but they are also moved slightly forwards due to the angle of the head tube. This combined effect will have you stretched out more as well as bent lower.

As far as saddle level goes, it's really hard for anyone to make a suggestion that will just work for someone else. I have my saddles so that they're pretty much horizontal. That is if you stuck a bubble-level right in the middle of the saddle it would read neutral. I have heard that most saddle companies design their saddles to be ridden this way but of course not everyone's body will subscribe to what some product manager in a cube thinks is the right saddle position. Unfortunately, this is something you'll have to play with. However, do it gradually and try to change only one thing at a time. Also, remember that when you move your seat post up or down, it also slightly changes fore-aft position of the saddle and so you may need to compensate for that.