Self Billing from Client- Private limited

Hi,

I am working as a contractor (using private limited company) for a company. Company issues me self billing invoices. Although, I also generate the invoices but I am bit confused between them.
I generate Invoices on weekly basis and they generate self-billing after my timesheet approval and just before payment, so got different dates on both.
Also the invoice number on my invoice is different from their self billing invoice (it is their internal number system),
Next year i m due to apply for my ILR after completing 5 years on Tier-1 general. I am just wondering what shall I use for my company earning. (Their invoices? or my invoices?). Also do I need to sign my invoices?
And also I am taking my profit as dividends (for my earning) as I have already reached threshold of minimum salary through my employment earlier. is it okay to do that?

Kind Regards,

Just wondering no body faced the similar issue in the past?
Senior... please reply