There are two issues relating to the balance of subassembly items that you will want to consider.
Negative on hand balances of subassemblies: QuickBooks allows you to make adjustments to inventory that can drive the on hand balance negative. This is a situation that should be avoided if at all possible, as QuickBooks does not handle it well. This could create problems with your COGS calculations and certain reports (there are several knowledgebase articles on this in the QuickBooks support web site).
If you have a negative on hand balance of a subassembly and you issue a full level build in CCRQBOM, the program will try to build enough subassembly items to make up for that negative balance. For example, if the program needs 2 subassembly items, but the on hand balance is -1, the build will be issued for 3. Without this, CCRQBOM cannot issue the high level build. If it only built two you would not have enough on hand to build the higher level assembly.
Subassembly balances: This is the opposite problem to the negative on hand balance issue. If you need two of a subassembly, but you already have one on hand, how many should the program build? There are two trains of thought here.
1. Some businesses will not want to use that available item. The build should be for two subassembly items in our example. That available balance may be an item that was built to fulfill a repair order, for example.
2. Other businesses will want to use that available item. It is there, use it! So CCRQBOM should just issue a build for one subassembly in our example.
To address this issue CCRQBOM has added a check box titled Use SubAssembly Balances.

If this box is checked, the program will use any available balance of a subassembly it finds.
If the box is not checked, the program will ignore the available balance of subassembly items.
The default value for this check box can be set in the Preferences function.