I would start with a small amount, such as 1 ml and use it subcutaneously. Just watch out, tonight I tried it out on myself because sometimes my dog seems uncomfortable when I inject it and then I realised why. It burns!!! It may have been a wrong location (I tried it in my arm). I don't have any specific information regarding trying to treat lyme disease or chronic fatigue syndrome with this, so I am sorry that I can't be of more help.
Use the morning urine - best time to collect is between 4 and 6 am, after that the urine is usually very strong. You might consider drinking it as well - if you decide to use the morning urine and drink it immediately.
I have found that with my dog (as an injection) it is easiest if the urine is nice and cold (i.e. it has been in the fridge for an hour or so).
You will need to test around a bit to see what suits you best.