There's a few ways to do it. The most intuitive is the following:

for (my $i = 0; $i < @a; $i++) {
    # Do stuff with @a and @b
}
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Another way would be to make a temporary hash and use each. This means you don't care what order stuff is done in, so long as the Nth element of @a is processed with the Nth element of @b.

my %temp;
@temp{@a} = @b;
while (my ($a_val, $b_val) = each %temp) {
    # Do stuff with $a_val and $b_val
}
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The first is clearer and easier to work with. Plus, it allows the addition of some @c later on in the future.

Now, if these are parallel arrays, you might want to consider doing the following:

use mapcar; # This is on a node [tye] posted somewhere on PM

my @temp_arr = mapcar { \@_ } (\@a, \@b);
foreach my $vals (@temp_arr) {
    # Do stuff with $vals->[0] (from @a) and $vals->[1] (from @b)
}
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That makes it very clear they are parallel arrays. *shrugs* YMMV

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Don't go borrowing trouble. For programmers, this means Worry only about what you need to implement.