If you're trying to insert a script then I'd suggest using the built-in functions of XSE or PKSV (which ever your choice is). By writing '#dynamic 0x800000' or '#dyn 0x800000' respectively. This sets an address in the ROM from where the the tool will instantly start to search for free space. If you're using FR then 0x800000 is a good adress to start from as there is tons of free space from that point onwards - Sorry, but I don't know R/S/E's best starting offset off the top of my head.
I would advise against deleting/ overwriting scripts that are already within the game unless you know what you're doing.
Is there any real difference between using a free finder to find open space on a ROM, and just starting from 0 and saving over existing scripts as you go? Would doing the second method save over the script for scratch or using the pc or something?