で (totals and groups)
altogether, as a group of
Amount / number of people + で
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で after an amount or a number of people draws a boundary around it:
- A total: 全部で三千円です, "that's 3,000 yen altogether"; 三つで五百円, "three for 500 yen".
- A group doing something together: 二人で行きました, "the two of us went"; 家族みんなで, "as a whole family".
- 一人で: "on your own".
It's the same で as "by means of", stretched a little: the group is how the thing gets done.
と can't replace it: 二人と would need a partner ("with two people"), and 全部と isn't a phrase at all.
Examples
全部で三千円です。
That's 3,000 yen altogether.
りんごは三つで五百円です。
Apples are three for 500 yen.
家族みんなで旅行に行きました。
We went on a trip as a whole family.
二人で映画を見ました。
The two of us watched a film.
一人でできますか。
Can you do it by yourself?