Are you asking about large muti-nationals like Honda or GM or little start up companies or something in between. I have been part of two smaller manufacturing companies, one was a start up?

At the start up we just kind of figured it out for ourselves and did things as cheap as possible while we figured out what we were doing.

At the older small company that I am work at now, they have done basically the same thing.

Companies with more capital hire industrial engineers to design the processes.

I have found that once you set up a few lines you start to find who the companies are that make the machines you need for your industry.

consider budget
consider location
take other things specific to your industry/field into consideration
research
research
research
finalize location (country, city, region etc.)
checkout existing blue print/ or new blueprint from architect
buy land/building/Old Factory (depends on the product you want to produce) and
build/modify new building/s or existing one
get appropriate permits from the city/ ok from mob boss
do safety checks
do power checks (most probably you need more power. You Always need more power)
more inspections (if moving into a new building, sometimes done before purchase)
receive the machinery you ordered in step 5
pay for machinery -wait 30 days then pay :)
watch technicians install/test machinery
get launch for technicians
panic
receive more equipment (ordered in step 5) (ex. forklifts, pallet jacks, shipping labeler)
Pay in 30 – 90 days
receive office equipment (chairs, desks phones) Pay 30–90
order some people around (the ones you interviewed and hired in step 5)
receive raw material (depends on the product)
test new machinery
have someone sweep the warehouse/factory etc.
invite IMPORTANT people for the opening
take pictures
cut ribbon
eat cake
panic
turn machine on (let them touch it)
kick everyone out (politely)
panic
sleep in the office
sweat
wake up
receive more equipment
receive more materials
finalize procedures
start the REAL production (Ribbon ceremony was for Show)
paint the office eggshell white
get high on paint smell
do the quality control on the first batch
keep the first item produced (depends on product)
ship first item/load item in trailer
sell an ok amount
get used to everything
watch sales go down
call and yell at sales guy/s you hired in step 5
remember you have a family (N/A for some)

it all depends on what exactly you’re trying to do, but having good people and taking care of your people is #1
It’s all about Research, planning and experience
After the first time, it’ll be much easier

Also as far as the “design”, you basically have a FLOW, the Raw material comes in from one end (docks etc) and goes through the plant and out the other end.
For the Machinery “design”, you just go to the appropriate company and either buy/lease it from them, Or have them make a custom one for you

good luck