Generally speaking this is not very difficult. The periodic boundary conditions only apply to the electrode, and so you place the caps in the central region, like so:
===========> ... <=============
| |
where = symbolically means nanotube, < and > are hemispheres and ... is whatever you wish to place in the central region. The vertical lines indicate the boundary between the electrode and the central region.
Does this resemble the kind of geometry you wish to set up?
Now, to do it in practice, all you really need are prepared hemispherical caps (say, as xyz or another molecule file), then you put a nanotube from the Nanotube Grower into the Atomic Manipulator, cleave it, and insert and align the caps.
I can give some more details if needed.