In PLUS RepliCAM after all four marked reference point on picture create a rectangle. You have to give size of that rectangle ie Length and Width which is most mandatory think to enter that select 'Settings > References > Set Rectangle Size' or click on icon present in reference toolbar. From which you can enter the distance which you take between references. In this case you will get a dialog box shown below.
you just select custom from combo box then enter size.
Also some you uses some reference size rectangle many times so you have add its length and width frequently. To avoid this you simply add this size in table. For that select 'Settings Menu > Save Standard References'. You will get a dialog box which contain a table as shown :
In above figure the table contain four columns Name, Length, Width and Remark you add data relative to that and save it. To add new row go to last row and last column and press 'TAB'.