$ cat pm_1232611.pl
use strict;
use warnings;

my %replacements = qw( FOO fubar    BAZ bazoom    BIM Kaboom! );
my @strings = (
   "what a %%FOO%% for a %%BAZ%%",
   "Eenie, meenie, minie, %%BIM%%",
   "The quick %%RED%% fox..."
);

for my $str (@strings) {

    print "INPUT: <$str>\n";
    my @vars = $str =~ m/%%(\w+)%%/g;
    for my $var (@vars) {
        if (exists $replacements{$var}) {
            $str =~ s/%%$var%%/$replacements{$var}/g;
        }
        else {
            print "Warning, no replacement for %%$var%%\n";
        }
    }
    print "OUTPUT: <$str>\n\n";
}

$ perl pm_1232611.pl
INPUT: <what a %%FOO%% for a %%BAZ%%>
OUTPUT: <what a fubar for a bazoom>

INPUT: <Eenie, meenie, minie, %%BIM%%>
OUTPUT: <Eenie, meenie, minie, Kaboom!>

INPUT: <The quick %%RED%% fox...>
Warning, no replacement for %%RED%%
OUTPUT: <The quick %%RED%% fox...>