You can use a PCR product floursecntly labeled, the problem is if ti is not for repeated region and you have just one copy of it in the genome that you are not going to be able to visualise it. If you have a huge amount of repetitions there then there is no problem. It docent have to be in the BAC even better if it is not. The role of the BACs is just to amplify it with less chance of mismatching of nucleotides and introducing errors, but if you have it already  don't worry about the BACs.

Hope this helps

Katya