Being a director of two companies in receipt of two salaries requires that you complete two “Employment” sections of your annual personal tax return. Similarly if you receive benefits in kind (such as a company car or health insurance) two forms P11D will need to be completed. You may also be in receipt of dividends from both companies, which will need to be included on your personal tax return.
As far as your tax liability one of the “Notice of Coding” received from HMRC will give you your annual personal allowance (£6,475 in 2010/11). The code number will be followed by the letters BR for Basic Rate or DO for the 40 per cent rate. Tax at 40 per cent will start on earnings above £43,875, unless you are over 65 years old when it increases to £46,890.
You need to talk to your accountant about how to maximise your income from both companies. A combination of salary and dividends will probably be best, assuming both companies have the cash and the profits to pay dividends. There may be other ways of minimising your tax liability but they depend upon the circumstances of both companies and your personal situation. Advice from an accountant familiar with both would be wise.