It is easy to align or stack members using the "Align Members" tool.
After selecting the members to be adjusted, right-click and select "Member Tools" => "Align members" from the popup menu that appears and then click another member to align them with. In the form that appears you can then choose to align the members according to their tops, bottoms or sides. Alternatively, you can stack members side by side or on top of one another using the "Stack" options.
In the before and after diagrams below, the blue beam has been adjusted to align with the red beam's top flange.