I use @BertieBotts's cheaty method one. I say cheaty method because YNAB is intended to be used for one account because the categories remove the need to keep separate accounts for savings.
So, I have a main account and two savings accounts. I do this:
~Set main category groups
~Set a main category group called 'Account 1' (mine is named, it doesn't matter either way) with a sub category savings
~Set a main category group called 'Account 2' (ditto above comment)
I add accounts 1 and 2 as checking accounts. Using a worked example:
Account 1 has £250
Account 2 has £800
In my budget, the category 'Account 1 - savings' has to have £250 assigned to it. 'Account 2 - savings' has to have £800 assigned to it.
If I spend £100 on clothing from Account 2, I enter the transaction as normal, but when I assign it in the budget I use the 'account 2 - savings' category to assign the money, so that category drops to £700.
If I forget to do that, and it comes out of 'ready to assign', then I make a manual adjustment to the category 'Account 2 - savings' by typing in -£100 to the assigned box, which has to effect of moving £100 out of that category into ready to assign, which balances the budget again.
Basically, as long as your savings category has the same value as the amount in your secondary account, then your budget will be sound.