District offices will communicate about the location of the crimes and the affected jurisdictions. These are not usually discussions defense attorneys are a part of.
Rules for jurisdiction and venue are set out in the Federal Rules of Civil Procedure and its companion Federal Rules of criminal Procedure. I suggest you go there for your homework assignment.
Typically they make a decision as to where most of the crime occurred, or which prosecutor's office did the investigation. They could prosecute them in either place. Sometimes, the place where most of the investigating officers or witnesses are is the factor. Many times in fraud cases like you suggest, there are victims in many jurisdictions all over the country. The prosecution will likely take place in the jurisdiction where most victims were, or where the investigation originated. There's no science to it, it's a judgment call.
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Usually where most of the evidence is located for convenience of all involved. However, as you pointed out this can be complicated and could be prosecuted in either location depending upon the situation.
The decisions are made by experienced federal prosecutors base on multiple factors and policy. The AUSUs (Assistant U.S. Attorneys) who are assigned to investigate and bring the information before Federal Grand Jury are under the supervision of attorneys who have extensive experience in particular type of criminal enterprise. The supervising AUSAs report to other even more experienced lawyers. The investigation is conducted by federal law enforcement officers from the FBI, DEA, IRS-CID, U.S Postal Inspectors and many other highly trained and experienced persons.
I realize that this response does not really address your question. The purpose of my response is to emphasis that the government has extensive resources and assets at their disposal to assist in the decision process. If your question is hypothetical then significantly more context is necessary to respond. If your question is based in fact and concern please cease using a public forum and consult an experienced federal criminal defense lawyer ASAP.
Of course, every answer or response is based on the information provided in the question asked and requires a much more complete context than is available in this public forum. This answer/response should NOT be relied upon to make any legal decisions. Seek the advice of an experienced Federal and/or state criminal defense attorney in your jurisdiction BEFORE you say or do anything.