It sounds like you want users to be able to directly key the account number if they know it, or else look it up using a drop down list (if they have Admin Permission level)
No problem,
Make a formula numeric field for the reference field on the relationship as the final relationship.
So you will have your existing relationship, but do not pull any lookup fields (nor make any summary fields) from that Relationship.
Then make a new relatioonship and for tyhe rerfence field on the right hand side use a fomrmula field like
IF([Account # (direct entry)] >0, [Account # (direct entry)], [Related Account #])
ie have a formula to use either the direct keyed account or the lookup account from the drop down list.
