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Your question is not clear to me but still i would like to give a try based on what i understood. I strongly believe no software could help your inventory or materials if you do not have an complete information of available materials on ground so in order to get the complete information we should do the following
1) Complete survey of the materials available in warehouse.
2) Upload the complete information according to the setup of the warehouse in the ERP system (specify Bin or rack number for better understanding)
Manual Warehouse system is like Man to Good even though your resources are fully involved in the process but still it is more time consuming where as software system warehouse is entirely depend on the information you feed to the system but it will save time and man power.
No program does not matter .. The best use of the programming system for the manual system