You can use destructive methods like GUS based detection of the expression of your gene of interest. I think this is the good methods instead of fluorescent-based methods.
Hum, what's the purpose of expressing those genes ? If you want to know where in the cell (e.g. nucleus, ER, Golgi, tonoplast, etc) your protein is expressed, GUS will NOT work. GUS is good to tell you in which tissue or which part of a tissue but its not as fine as FPs. Whatever the FP you choose (CFP, YFP, GFP, RFP) in plants you will have autofluorescence. With a good confocal microscope it is usually not a problem. I would go with GFP, YFP or mCherry since they are quite bright. The trick is to choose your tissue well, you need a young and thin tissue. For instance in Arabidopsis 2-3 days old cotyledon is best, with Nicotiana I do a leaf epidermis peeling because its too thick, with poplar I do strips.