Create a stack and add a field, name the field "display".

Add some text to the field, in this example I have used the first paragraph of Alice in Wonderland, and have deliberately misspelled some of the words.

You can use a chunk expression to flag any piece of text.

In this example the word 'begining' is misspelled so we want to flag it. It is the 3rd word of the field so you can run this in the message box:

set the flagged of word 3 of field "display" to true

You can use any chunk expression so you can flag lines, ranges of text, for example

set the flagged of line 1 of field "display" to true
set the flagged of word 3 to -1 of line 2 of field "display" to true

You could run this in the card script, using

on openCard
   set the flagged of line 1 of field "display" to true
end openCard

Now if you close the stack and open it again, the first line will be flagged.

You can also flag, or unflag the current selection using the selectedChunk function.

Add two buttons to the stack, one to flag the selection and one to unflag the selection.

The script of the "Flag Selection" button is

on mouseUp
	set the flagged of the selectedChunk to true
end mouseUp

The script of  the "Unflag Selection" button is

on mouseUp
	set the flagged of the selectedChunk to false
end mouseUp

Now highlight a piece of text and click the "Flag Selection" button.