Could you please separate it into two or three bags next time?
Do you mind putting everything into a few different bags from now on?
ーCould you please separate it into two or three bags next time?
「次は、２つか３つの袋に分けて入れてもらえますか？」
to separate で「〜に分ける」
ーDo you mind putting everything into a few different bags from now on?
「今度から数袋に分けて入れてもらえますか？」
to put ... into a few different bags で「…を異なる数袋に入れる」
ご参考まで！
カナダ 
