You copy the reference designator and paste it into the Value field of the Unfitted parameter, Note, The reference designator and the Value field of the Unfitted parameter need to match each other.
You can turn off the visibility for the parts other parameters,
Cross check any information in the Unfitted column for reference designators that are different than what is shown in the Reference Designator column, IE. C4 in the list C1, C27, C44.
Look in the Unfitted column for any [NoValue] and remove them,
Save the changed file.
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Make or open a separate library for your Assembly designs, This will become a very large library very fast and you do not want it to conflict with your main library or libraries.
After you have completed the design for the daughter board,
Open the daughter board design and pull down the File menu from the top,
Select the Export sub-menu and slide right, then select the Step 3D sub-menu,
Chose the name for the daughter card assembly and put it into the File Name box, Make sure that you include the step extension and make a note of the data path.
Click on the OK tab,
After the script is run, click the OK tab to get out,
Navigate to the daughter card database, select the step file and click Open,
Rotate and position the 3D image so that the Pin 1 is positioned in the center of pin 1,
Select the pad and copy it, then Paste it onto all of the other pins positions, If you setup the grid for the pin to pin spacing, you can set the pins faster.
Renumber the other pins to match the connector that is on the daughter card,
From the PCB Library menu, highlight the footprint,
Add the an outline of the board and connector to the top silkscreen layer, The 2 outlines will help place and show where the daughter board goes.
Right mouse click and rename the footprint to the name and description of the assembly footprint,
Place the daughter board in the position on the main board,
Setup your Main board Design Rules for the Placement Component Clearance spacing, This gives you the 3D clearance between the Daughter and the Main board.
From the top menu, select the Tools and pull down the Reset Error Markers,
Now from the top menu, run the Tools Design Rule Check and click on Run Design Rule Check,
You can add and use hidden parameters in your library parts to help filter BOMs.
You can hide or keep parameters hidden in your schematics to help explain which parts are or are not to be used.
The hidden parameter Unfitted is compatible with the Variants Sub-routine.
You can do copy/paste and rename in the schematic part of the library.
You can use Tools, Parameter Manager to globally edit and update the SCH library.
Due to the use of mixed technologies, few BOMs can be used for everything.
You may need 1 BOM for the assembly of all SMT components on a PCBA, another for the Thru-Holed components on the same PCBA and you may need to divide, subtract or cross reference Not/Assembled (N/A) parts.
Altium Designer can output a master BOM that can be separated into all of the BOMs talked about above.
You can use the Excel Auto BOM Filter template to do the filtering.
You can simply create Sub-Assemblies of daughter cards and add them into main PCB designs.
You can run a 3D DRC to verify that there are not any conflicts between the main PCB and any daughter cards.