Assuming your locale supports thousands separators (and many do not) and you are using gawk (GNU awk) and not awk or nawk the following will do what you want

$ cat t.awk
{ printf "%d@%'d\n", $1, $2 }
$
$ cat file
1@1000
2@2000
4@4000
5@7770
6@8998
7@80008
$
$ gawk -F@ -f t.awk file
1@1,000
2@2,000
4@4,000
5@7,770
6@8,998
7@80,008
$