You can easily program any default paths into your LabVIEW code, or read them from an ini file. There is no need to jump through any flaming hoops.
Properly written, a VI can do anything you want with one single click! 😄 (or even without any clicks at all! 🐵
(You could probably leave Matlab out of it and do the analysis directly in LabVIEW code. If you have LabVIEW 8.0, you could even re-use some of your matlab code using mathscript, but it might be equally easy using wires only.)