Depends, the main factor is what do you really like? If you feel that the cabinetry you chose doesnt look good if cabinets do not align vertically, then line them up. If its not possible try a different cabinet design that you like that looks good to you even if not aligned.
I usually try to keep cabinets aligned but it really depends. But its your kitchen so do what you think looks good.
Absolutely not. Base cabinets are all about function. Wall cabinets should have the doors as close to the same size as each other as is possible ( secondary to function of course ). It would be ridiculous, for instance, to have a 9"wall cabinet next to a 36" wall cabinet just because there is a 9" tray base and 36" pots and pans drawer cabinet below. A "designer" who does this is demonstrating an inability to see in 3 dimensions.Run from them. This kind of thinking was old even 20 years ago and is inexcusasble when cad systems can give dimension to typical downview floorplans!
