I'm afraid the 'best way' to debug anything depends on what you are debugging, what the exact problem is you are debugging, and your debugging preferences. So I'm afraid I can't give you the 'best way'.

I sometimes use a debug switch in my code at critical points like:

my $DEBUG=1;

...

my $val = get_something("vars");
warn $val if ($DEBUG && ! $val);

...

my $val2 = do_something_else($val);
warn $val2 if ($DEBUG && $val2 =~ /^\w{2}\d{2}$/);
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This way you can turn off/on debugging by (un)setting the master-switch $DEBUG, and even use different $DEBUG values for different types of debugging, the sky is the limit.

If you want to see the call tree of your program you could use Devel::Dprof.

If you want to see the content of complex structures, you could use Data::Dumper.

Some people really like the perl debugger, you can do some cool tricks with it, see the perldebug docs.