Good practice when designing a PCB and stencil?
well for easing the alignment I usually make some two '+'(plus) signs at two sides of the PCB I draw those plus signs as multi-layer in Altium designer so it will be on the stencil too.
one more thing is using a transparent stencil so that you can see the other side 
and If you are making lots of PCBs, it is profitable to buy a stencil than to make one 
but remember to ask the operator not to cut the PCBs to pieces so that you can put the components all at one try it is  a lot faster

another way is that you can also just export your pins as a CAD file and send if for a laser cut on a 0.5mm It will cost you much less.