You make your attacks one at a time.
Here is what the rules say regarding attacks:
The most common action to take in combat is the Attack action, whether you are swinging a sword, firing an arrow from a bow, or brawling with your fists.
With this action, you make one melee or ranged attack. See the "Making an Attack" section for the rules that govern attacks.
Certain features, such as the Extra Attack feature of the fighter, allow you to make more than one attack with this action.
Making an Attack
Whether you're striking with a melee weapon, firing a weapon at range, or making an attack roll as part of a spell, an attack has a simple structure.
Choose a target. Pick a target within your attack's range: a creature, an object, or a location.
Determine modifiers. The DM determines whether the target has cover and whether you have advantage or disadvantage against the target. In addition, spells, special abilities, and other effects can apply penalties or bonuses to your attack roll.
Resolve the attack. You make the attack roll. On a hit, you roll damage, unless the particular attack has rules that specify otherwise. Some attacks cause special effects in addition to or instead of damage.
You declare that you are making an Attack action, and pick your first target, determine modifiers, then resolve the attack. Then you begin making your second attack, pick your next target, determine modifiers, resolve the attack. Finally begin your third attack, pick your third target, determine modifiers, then resolve the attack.
When Two Weapon Fighting, the additional attack is a bonus action. It does not happen simultaneously.
When you take the Attack action and attack with a light melee weapon that you're holding in one hand, you can use a bonus action to attack with a different light melee weapon that you're holding in the other hand.
With the Extra Attack feature you can make two attacks when you take the Attack action. This does not force you to roll them simultaneously, you take one then the next.
Rolling multiple attacks at once is for convenience to speed up combat. If you play with this house rule then your DM may come up with a way for you to use the excess die, but there are a number of questions.
- Normally attacks happen in order, so miss, miss, hit, dead is different to hit, dead, 2x attacks can be directed elsewhere. If you rolled 2 misses and 1 hit, killing the enemy, do you expect those 2 misses to be "excess", to be redirected somewhere else?
- If you are rolling damage and attacks together, how do you determine which damage belongs to which attacks?
- If you can redistribute attacks after rolling them, then can you choose to put them on targets with AC low enough that you know you will hit? Do you need to reroll them when redistributing them?
Some suggested solutions:
- Roll multiple colors of die; eg red is your first attack, green is your second, blue is your third. Then you can tell when you killed the enemy and which attacks are leftover. Suggested by V2Blast (go give them rep!)
- Just don't care. Depending on your encounters it may be rare for the situation to ever cause any advantage. Suggested by KRyan (give them rep too!)
In my opinion, is it best to roll 1 at a time. But if you do want to roll all at once, then you have the inherent disadvantage of possible overkill.