Do i have to make the array declarations before i take their reference or can i do that at the same time?

You do not need to declare (or even name) the arrays at all.

When you push or assign to a complex data structure the intermediate aggregates will be autovivified (Ie. created if they do not yet exist.):

my %main_file; 
push @{ $main_file{ USER }[ 1 ] }, 'fred'; 
push @{ $main_file{ TEST }[ 3 ] }, 'bill'; 
push @{ $main_file{ TRIM }[ 0 ] }, 'john'; 

pp \%main_file;;
{
  TEST => [undef, undef, undef, ["bill"]],
  TRIM => [["john"]],
  USER => [undef, ["fred"]],
}
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