As long you as have deposited back in the account same day before midnight it won't effect the account as reports are generated every day after midnight.
Book on booking.com and choose the option to pay at the property. They will send you a proper confirmation which will be sufficient enough to apply for visa.
If he has good command on GDS and can do ticketing & stuff then the best option would be setting up a small business on your name since you are Thai Citizen. Travel industry has a lot of potential in Thailand. He can make a website and offer tickets, hotels, tours to tourist coming from UK/Ireland.
There is no visa on arrival for Pakistanies. You have to apply in advance. 4000 PKR is consulate fee and Travel Agent will charge another 2000 rs for the services. However you need the following supporting documents
1- Return ticket ( Travel agent will arrange it for you )
2- Bank statement of last 1 year with a minimum closing balance of 100,000 PKR
3- Hotel booking ( Travel agent will arrange it for you )
4- NTN
5- Employment proof ( A letter from the employer stating your designation, tenure and salary )
Your profile says that you are in Karachi, there is a Royal Thai Consulate in Karachi. Either you can apply visa directly in consulate with all the required documents or you can apply through a travel agent.