Associating two vault items with a single component in Altium
The whole bomdox system does only work if you by the items and assemble the board. It does not work anymore if you by the complete assembled board from a company and this company byes all the resistors, capacitors, ...

Because of this we don't use bomdoc. We define a "generic 1k 0402 Resistor" in our lib/vault. There we add parameters for every Manufacturer. (as many as we like)
Manufacturer1, Manufacturer_PartNum1, Manufacturer2, Manufacturer_PartNum2, ...

Additionally we have some non generic items like "Panasonic 1k 0402 Resistor" which has only Manufacturer1, Manufacturer_PartNum1

By this the Designer can choose if uses the generic resistor and allowed all the alternative parts or chooses a special one where no alternative is allowed. The advantage AND disadvantage is that a different project also gets them automatically.

This can be exported to an XLS Bom and sent to our supplier of the assembled boards. In this XLS we see then all allowed alternative parts, not just two solutions.

If you by all the components and assemble the boards by yourself you can also use the BOMDOC:

First you assign alternate parts to your items in the Bomdoc. 
e.g. 1k 0402 is by default from Panasonic

Your alternate Item needs to be an Item in your lib/Vault with its own Manufacturer &amp; Part number. 

With "split Item" You can define "Alternative Groups". By this e.g. R1, R2, R3 can be populated with 1k 0402 from Panasonic or yageo but for R4 only 1k 0402 from Panasonic is allowed.

After this you define the solutions. There you already define which resistor vendor is selected for each and every item. So again this works only if you are the buyer of the items. 

The XLS Bom from the bomdoc does only contain two solutions independent of how many alternate parts you have allowed.