Based on the discussion in this thread I've ignored the regexes in the OP and instead pieced together the various examples given.

#!/usr/bin/env perl
use warnings;
use strict;

use Test::More;

sub parse {
    my ($str) = @_;
    my @m = $str =~ m{
        ^ (?<P_ROOTCODE>\w+?)
          (?: (?<DAY1>\d)
              (?<P_MON_CODE>\w)?
              (?<P_NEW_MON_CODE>\w)?
          )?
        $ }x;
    note explain { $str => \%+ }; # debug output
    @m = map {$_//''} @m; # undef -> "" (optional)
    return \@m;
}

is_deeply parse("RS"), ["RS","","",""];
is_deeply parse("RC1XY"), ["RC","1","X","Y"];
is_deeply parse("RW12QW1X"), ["RW12QW", "1", "X", ""];
is_deeply parse("Sample1Repeat1A"), ["Sample1Repeat", "1", "A", ""];
is_deeply parse("Sample2Repeat2"), ["Sample2Repeat", "2", "", ""];
is_deeply parse("Sample3Repeat"), ["Sample3Repeat", "", "", ""];
is_deeply parse("4SampleRepeat"), ["4SampleRepeat", "", "", ""];
is_deeply parse("4SampleRepeat4"), ["4SampleRepeat", "4", "", ""];
is_deeply parse("5SampleRepeat5D"), ["5SampleRepeat", "5", "D", ""];

done_testing;
[download]

Sample output:

# {
#   'RS' => {
#     'P_ROOTCODE' => 'RS'
#   }
# }
ok 1
# {
#   'RC1XY' => {
#     'DAY1' => '1',
#     'P_MON_CODE' => 'X',
#     'P_NEW_MON_CODE' => 'Y',
#     'P_ROOTCODE' => 'RC'
#   }
# }
ok 2
# {
#   'RW12QW1X' => {
#     'DAY1' => '1',
#     'P_MON_CODE' => 'X',
#     'P_ROOTCODE' => 'RW12QW'
#   }
# }
ok 3
...
ok 9
1..9
[download]

If that still doesn't suit your needs, add more test cases.