To align any object in Photoshop relative to a bounding selection, do the following:
- Click on the layer containing the objects you want to align
- Using the selection tool, create a selection.
Normally, if you want to align objects relative to the entire canvas area, select the entire canvas area (CTRL+A) - Click Layer > Align Layers to Selection and then click on an alignment option
This will leave you with perfectly aligned objects.