Have a look at these articles

a) https://www.biorxiv.org/content/biorxiv/early/2018/05/01/312207.full.pd

b) https://www.osapublishing.org/viewmedia.cfm?uri=ao-55-22-5967&seq=0

c) zeiss-campus.magnet.fsu.edu/.../pdfs/Davidson_Abramowitz_Optical_Microscopy.pd

d) Article Binary phase masks for easy system alignment and basic aberr...

e) https://wp.optics.arizona.edu/optomech/wp-content/.../sites/.../Article-for-W.Cai_.pd

The following links are very useful:

https://onlinelibrary.wiley.com/doi/pdf/10.1002/9783527671595.app1

http://post.queensu.ca/~chinsang/lab-protocols/proper-alignment-of-the.pdf

Depends on what you are working with?

are you talking about the optical path or the beam inside the microscope itself?

Both