that's a lot of questions.
And what happens if I withdraw all my BTC from my wallet? I cannot have a negative balance, so will my payment order be diminished? Does it always happen this way?
if you withdraw all btc you'll be left with 0 balance. electrum won't allow you to send btc if you don't have enough balance. you can't get negative balance.
don't even know what you mean by "always happen this way"... have you experienced it?
And most importantly - if I want to make a payment of a precise amount, will it be affected? How do I ensure that the desired amount is being transferred from my wallet if I don't know the fees?
what you enter in the "amount" box doesn't include the fee. the fee is deducted separately from what's left in your balance.
you can view electrum's estimated fee before you send anything by ticking the "Set transaction fees manually" option from preferences. electrum will still suggest what fee you should use even if you have that option on.
[1] input*148 + output*34 + 10 . this can get really off-target for transactions with lots of inputs and outputs.