Thanks for helping to build our global tree here and for adding your DNA test info to your profile.
Per the Y-DNA Confirmation help page to which Peter linked, once you've determined that a match meets the criteria for DNA confirmation, "you can mark the paternal relationships as Confirmed with DNA" (see the "How to Mark Relationships as DNA Confirmed" section of the DNA Confirmation help page which is linked from the Y-DNA Confirmation help page for more details, if needed). Marking parental (paternal and/or maternal) relationships as "confirmed with DNA" will cause the yellow DNA box with the green check mark to appear in the appropriate places on parental relationships in profiles, in tree views, etc. Is that the "flag" to which you're referring?
Also, per the same Y-DNA Confirmation help page to which Peter linked, "Here is an example of what to add to the == Sources == section of each son with a father marked "Confirmed with DNA" using yDNA". So the DNA source confirmation statement goes in the Sources section of each son's profile for which you've set the paternal relationship indicator to "confirmed with DNA". I usually place it at the bottom of that section of each such profile, but it just needs to be in the Sources section. You can optionally add a === DNA === subsection to the Sources section, in which to place the confirmation statements, if desired (again, see the same DNA Confirmation link from the Y-DNA Confirmation help page for more details).
Please let us know if you still have questions.