Well, I could start by saying that the first best way is to use FireBreath instead of nixysa, but that would be rude and could cast aside my preconceptions ;-) Seriously, however, there is nothing wrong with nixysa; I highly recommend FireBreath that it works on both IE and Windows and has a lot more fixes and workarounds to make sure everything works on all browsers and platforms.
There are many suggestions for debugging plugins in general (as when attaching debuggers to them) on the FireWreath wiki , which all work very well with any NPAPI plugin.
Getting debugging methods, such as working with linux, can be especially painful, so on linux I tend to be more inclined to use a logging framework like log4cplus .
Others may have more suggestions, but this will probably help if we know exactly which platforms you are targeting; for example, Chrome (I noticed that the tag in the question) supports the -plugin-startup-dialog parameter, which is invaluable for attaching to the plugin before its launch due to the multiprocessor nature of the plugins in Chrome. IE and Firefox have options for disabling OOP plugins (outside the process), which simplifies their connection.