Inventory
Set up good item coding (item ids, aka sku's, product numbers, part numbers etc.) Don't use long codes, don't use special characters (problematic for future bar code implementations or integrations to other systems).
Print and label physical parts or their boxes with codes. Also include receipt or work order information on the labels which can help resolve mislabeling issues later.
Do not use supplier or OEM part numbers as your own part numbers. There are places for this data which is linked to items appropriately.
Numeric or alphanumeric part numbers? There is no correct answer. One option is to match product part numbers to product id's used in your marketing and use sequential numbers for everything else. It gets hard classifying parts with part numbering and there other other tools for classifying parts into groups.
Have good, clear housekeeping for material controls. That means logical shelving and bay locations.
Mark shelves with magnetic tags, not with stickers, so you can reorganize later.
Consider your policy for sub-assemblies. A clever design of sub-assemblies in manufacturing can greatly enhance the performance of the over all business by reducing lead times and inventory values.
Production
Keep in mind "lean" manufacturing. Make work orders as small as possible so that their throughput time is short as possible and they can be closed as soon as possible.
Identify and mark work cells in production areas. Do good house keeping.
Avoid part completing work orders. If you are doing this, you probably should be doing smaller work orders.
Use automation tools such as bar coding and bulk work order creation to help streamline a lean manufacturing flow.
Use dedicated work order only when physically different products are being made under that same item id. Manu Online has an allocation system for in stock orders that works well with rolling call-off contracts.
If your customer is giving large sales orders with multiple delivery schedules, consider using tentative order forecasting and confirm sales orders only in a shorter time window for instance break annual call-offs to monthly confirmations.
Invoicing and administration
Connect your Manu Online account to your accounts system early and import partners, items and account codes. This will not make any changes to your accounts system, but it does make "mappings" of business objects between the two systems so that duplication is avoided later. Avoid the need of changing the connection later as it will need data to be cleared in your Manu Online account because of those mappings.
Implementation
"Prototype" business processes before taking them into use. Run with sample products. Use a separate test account if necessary. Do not assume that the details of Manu Online work in the same way that your previous system. Either things are just different, or hopefully Manu Online has better ways of working that you can take into use.
Work with just one or two representative products during prototyping. Manually enter these products before using any bulk upload tools.
Focus early on the sales order -> dispatch -> invoice process if it is too much to take the whole system into use at one time. Invoices are what bring money in.
However, if you need traceability, often this is best to get this from the start. It is tedious to later look at history and have untraced items out with customers.
Map out data flows for any integrations on a sheet of paper. Do not assume that an integration works in the same way that you think. Manually do the data flow of an integration before automating it.