The very first column (A) in the template is reserved for system-allocated indicator ID numbers.:

The second column (B) in the template allows you to specify links from your new indicators to any higher level indicator(s) that already exist:

Simply add the ID number of the indicator you wish to link your new indicator to. This method also allows you to both add multiple links (by adding comma separated ID numbers) and to remove existing links (by removing the relevant ID number(s).
The third column (C) in the template allows you to specify links between indicators even if they don't yet have an ID number, e.g., it allows you to specify links between different rows in the spreadsheet:

To create links between indicators (rows), use tiered heading numbers. Let's say you have four new indicators and your job is to create the following hierarchy. Example numbers for column (C) of the template would then be as follows:

That would be entered into the spreadsheet like this:

Note that with this method an indicator can only be linked to one other indicator on a higher level.