We have used the fluorescent dye, DiOC6, to label internal membranes
in living yeast cells. This dye also labels Chlamy. One of the
critical features of the labeling is that the cells must be alive.
Dead cells just stain non-specifically.
Although DiI and DiO have been used to label and trace neurons in
fixed tissue, exposure to the dye takes weeks (at least). I suggest
you try labeling cells while they are still alive and then
deflagellate and process the flagella. Alternately, Terasaki
dissolves his dye in Wesson oil and injects it into Xenopus oocytes.
Whatever membrane comes in contact with the oil droplet is stained
(he was particularly interested in ER). Perhaps using this strategy
(vortexing gently to allow the flagella to contact the oil drops,
then removing the oil when it floats to the top) wuld be successful.