@John ******
I've heard one or two offices in the country do things differently, however, the general rule is that during any 90 day entry, when you have less than
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(depending on office) days remaining, you can apply for the 1 year extension. There is quite a bit of paperwork required, so best to visit your local immigration office in advance to get a copy of their printed list of requirements and confirm their timing. This will include >B400,000 in a bank account in only the name of the foreign spouse, seasoned for 2+ months, photos of couple at home, marriage certificates, etc.
After applying for the extension there is a waiting period of a few weeks, during which time immigration will normally conduct a home visit, and then you return to the immigration office to get the 1 year extension stamped into passport.
After getting the extension, you can then get a re-entry / multiple re-entry that will allow travel in and out of the country.