Flouncy with your situation, I'll give you an example.
You have a brand new copy of YNAB. Set up the categories as you want them.
Now, you need to enter your starting balance of each account you will have on balance.
Say you have 2 bank accounts:
Acct 1: Balance £200
Acct 2: Balance £100
You create those accounts in YNAB and put your balances in.
So far, so good.
But you have that cash sitting in your house, right?
Well, you can keep track of them in your budget, by creating another on budget account. Simply add up all the money in your safe:
car tax £30
mot £25
Christmas £100
Holiday £550
Total: £655
So, you enter the starting balance of your new 'account', which you can name 'Safe' if you want to, as £655.
Then, you create categories of car tax, mot, Christmas and Holiday
You'll have £655 Available to Budget, so give every £ a job.
£30 is given the job of 'car tax', £25 is given the job of mot, £100 is given the job of Christmas, £550 is given the job of Holiday.
It's as simple as that!
YNAB doesn't care where the money is, as long as it's all accounted for and none of it is budgeted twice.