Depends is the honest answer.
To keep things simple I pay us the same amount each month, which should leave some in the business for van/equipment replacement and maybe enough for a bonus now and then!
I'm running a small surplus at the mo' which I have investment plans for.

The thing to remember is that you are legally the employee of a company and it's the company's money so you must account for what you do with it.
Profits are taxed once earned, and then when you pay yourself that money it's liable for the usual taxes that wages are, but of course with the help of your accountant you decide how you pay yourself (dividends etc) to make it tax efficient. I don't pay much income tax at all.
Also useful if you have kids and want to claim child benefit, or even child tax credits as your take home pay is basically the same as your earnings, but you can leave money in the business if you have a stonking year to pay yourself another time without it affecting them.
The advantage is you play it how you want and to suit you, the disadvantage is the higher accountancy costs and higher reporting requirements.
Oh and one last thing, stay honest with it (as I'm sure you would) the allowances are fine so you don't need to cheat and have to worry about getting caught.