it depends on the bacterial endophyte you want to tag and which plant tissues you want to detect it in and what you mean by activity. simplest thing would be to make a stable antibiotic resistant strain, inoculate plant host, homogenise and plate various tissues a week or so later and plate dilutions on to selective media, count colonies and job done. more elegant (nicer photos) If its easy to transform and stable after, you can electroporate in a flurescent protein and confirm presence in fine reletively transparent tisues like roots. this approch is already published been done with a Bacillus amyloliquefaciens sub sp plantarum FZB42 in Arabidopsis thaliana.

you can use Real-Time PCR with your bacterium -specific primers to find a number of alive bacteria in plant tissues.