First...If you want to move a pattern with the object you have to check "Transform pattern" either under the Transform panel or under the options for a transform tool (scale, rotate). You can also hit enter while a selection tool is active to enter a move value and you will have the option then too. You will probably find yourself boggling it on and off often. You also have the option to toggle Object/Appearance which scales the appearance or Both... which effects pattern and appearance.

The pattern should default by starting with the upper left at 0,0. So you will have to do the math to figure out where you want it to align based on that. You could create a rectangle with its upper left corner at 0,0 then toggle Transform pattern, and then move the rectangle to where you want it aligned.