THe shape of the tube should not affect the shape of the tire. The casing of the tire determines its shape and the tube simply stretches to fill that shape. If the tire is not shaped properly and it was before then one of two things could be happening: the tire is not 'seated' correctly on the rim (this is likely); or the casing of the tire is damaged and you have a bulge.

If it is a 'dip' in the tire then the correct fix is to let most of the air out of the tire, look between the tire and th rim to make sure the tube is not trapped somewhere, then and physically pull the tire out where the dip is, then spin the wheel to see if you have had any effect; if no effect, then pull it some more and check again. Often fully inflating or slightly over-inflating the tire will cause the tire to 'pop' into the correct position on the rim, but I do not recommend this as I do not know your particular set-up.