In practical terms you use ridiculously expensive computer controlled portable machine that just does it without much of manual intervention. It is done by such automatic splicers almost since fiber optics are used for practical applications. There were manual (mostly mechanical) splicers that are not too hard to use (it certainly requires less skill than above mentioned laboratory glassware), but it's more economical to just automate the task.
The problem is that even almost perfect splice incurs significant additional signal loss, so for long cable runs you do want to do smallest number of splices (and connectors, which are orders of magnitude worse) as possible.
Edit: To be more specific - do you have a quiet/stabilized optical platform onboard to perform this?
Across undersea long hauls, optical amplifiers exist (think repeaters, but without any introduction of delay). They get their energy from being pumped by a wavelength of light different from those used for data transmission[5].
1. http://www.idquantique.com/images/stories/PDF/network-encryp...
2. http://en.m.wikipedia.org/wiki/Evanescent_wave#Evanescent-wa...
3. http://131.238.119.245/asarangan/courses/542/student_project...
4. http://www.rootsecure.net/content/downloads/pdf/fiber_optic_...
5. http://en.wikipedia.org/wiki/Optical_amplifier#Doped_fibre_a...