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I have a table which requires it to be joined to a parent table in order compare it as its business key exists on the parent.

So I can write a custom query to do the comparison and that seems to work well. However, I'd really like this within a report. It doesn't seem like custom queries get written out to the reports.

Is there some better way of doing this, I would imagine that having to compare via a second table to get a business key is a fairly commmon use case?

Should I be using custom queries?

Is there some way get custom queries to appear in the reports?

Please note that the result of using custom queries is also included into comparison reports just like you work with tables or views. However, if a custom query is specified in the Target section of the 'Custom Queries Mapping' dialog box, then it can't be used in synchronization and the 'Objects marked for synchronization' option can't be selected in the 'Comparison Report' dialog box.