I have a holding company which owns 100% of two LTD companies let's just call them A and B
If I was to be paid from a company say ABC for work carried out by my company A does my company A have to issue an invoice to company ABC or can the holding company do this ?
The issue I have is that I would need to setup 3 different bank accounts to be paid into and from which could be a bit of a hassle after a while.
Normally it is the company performing the service that issues the invoice. (so company A in your case) The holding company's role is usually to consolidate the results of the companies A & B, not to send invoices...
Regarding the type of question you ask (and thus the level of your knowledge of accountancy), I must advice you to consult (and hire) an accountant. Because the things involving holdings etc. will become even much more complex than this one (e.g. tax declaration, intercompany cash flows, guarantees for bank loans...)
Another advantage of hiring/outsourcing an accountant is that he/she knows well all the local specificities that people in forums like this one doesn't always know.
Disclaimer: I am not an accountant