请问一个英语语法的问题

in the order 不是说排列顺序么，这个排列顺序就是指是在高级导出操作时所弹出的窗口中，你对这些列进行选择的顺序。

They 指的是 columns。

整句话的主语是 Advanced export to Excel, 谓语动词是 puts， 宾语为 columns，后面整体作为状语修饰puts，就在说如何的来puts。

后面状语部分中，order 后面省略了that, they were selected in the Advanced Export popwindow 修饰in the order。

原句完成结构应该是
Advanced export to Excel puts columns in the order that they were selected in the Advanced Export popwindow.

不知道这么解释你明白了么。

省略了 in which，理论上不够严谨,因为一般只有作宾语的which/that才在定从中省略，
in/on/at which一般不省略

应该理解为：puts columns in the order （in which）columns were...
定语从句修饰order，which代指order
they指代columns

就是定语从句，they were selected in the AE popwindow 定 the order。相当于中间省略了一个(which)。

选择Advanced export to Excel（高级导出至Excel文档）功能，可以将内容导出到Excel文档中，并且列顺序与在Advanced Export弹出窗口中所选择的顺序保持一致。

Advanced export to Excel puts columns in the order they were selected in the Advanced Export popwindow.
这句话的意思是高级导出excel（ Advanced export to Excel ）导出到excel的列顺序正是他们在 Advanced Export popwindow窗口选择的顺序一样