If it's your limited company, then you need to declare that onto your Form E as well. All you'll be doing is moving money from one bucket to another. Whilst typically she'll be entitled to half the business, if you set it up after separation you can argue that she's had no hand in it and therefore not entitled to half - an argument worth running but doesn't always work.
What my ex did was take £250 out of the cashpoint every day, and "spent it on ice creams" for the children - that's £7.5k per month under a mattress. The judge didn't care.