1) The cost calculation for Standard Cost is determined by what you establish on the Routing. The cost applied to the Prod. Order is based on how you record the entry in the Output/Production Journal. If you know a specific Machine Center will be used, you can update the Prod. Order Routing (doesn't change default Routing) to reflect the specific Machine used. In the Output Journal, when the explode Routing is used, or the Production Journal, it will list what is defined on the Prod. Order Routing. Lastly, you could manually record the entry in the Output Journal for the specific Machine used.
2) IF your Machines are all interchangeable, it is best to list the Work Center on the Routing operation. IF you need a specific machine (robo-welder vs. a human welder), then you would list the specific Machine Center on the operation. This becomes more important when you utilize a scheduling engine (App Source), as the Work Center allows for any Machine to be scheduled, whereas listing a Machine Center restricts the operation to that specific Machine.
3) The Routing Link Code associates specific BOM Items to specific Routing Operations. This helps with the need date for the material, and speeds up the backflushing of Items. When Output is posted against an Operation, any Items (backflushed) connected via Routing Link Code will be consumed at that time. If the Items are not linked via Routing Link Code the backflush doesn't happen until the Production Order is Finished. A similar consumption happens on forward flushed Items, but almost nobody uses that.
4) MPS is your Direct Demand, generally a Sales Order. MRP is your indirect demand, such as components (raw material or sub-assemblies) on a Production Order BOM. I am a fan of running both MPS and MRP at the same time. With the filtering capability it is easy to focus on what you need.
P.S. This is fairly high level information, but hopefully helpful. If so, please mark it as a Verified Answer to help other forum users. I would also strongly encourage you to reach out to your partner who should be helping you understand these capabilities in more detail.
Best Regards,
Ben Baxter
Accent Software Inc