I am not sure I understand what you are getting at here.
Irrespective of whether you use Edit-Clear all or not on a selected range,
when you select the Edit-Goto-Special-Blanks, that will select all the blank
cells in the current selected range.

A neat manual trick here is to use standard entry procedures.

So a demo for you and anybody else interested here:

Select a new sheet

Type 123 into cells:

A1, A4, A7

B2, B5, B8

C3, C6, C9

Click into any cell  within the range say  B5

Press the Ctrl+* to select the current range

Select Edit-Goto-Special-Blanks

Note the active cell, should be B1

Type in 999

If

you press Enter, the next cell is selected in the selected range moving down
to the end of the current column  & then up to the top of the next column

Else

you press Tab, the next cell is selected in the selected range moving to the
right to the end of the current row  & then down to the start of the next row

NB: if you make a mistake, hold the Shift key and press either Tab or Enter
to move back. If you click into the area with the mouse or use arrows you
will loose your selection & have to start again, but omitting any cells that
you have successfully entered data into.