Beyond Compare's Table Compare (default view for CSV and XLSX files) doesn't support manual alignment of rows. Rows are automatically aligned based on key columns.
The default settings make column 1 a key column. To change the column type, right click on a column header and select Standard Column or Key Column.
To change the row sorting behavior in the Table Compare, click the Rules toolbar button (referee icon). In the Alignment tab, select Sorted alignment, Unaligned, etc.
Beyond Compare's Text Compare does support manual alignment of lines. To open files in the Text Compare when they're already open in the Table Compare, select Session > Compare Files Using > Text Compare. In the Text Compare, right click on a line on the left and select Align With, then left click on a line on the right.