what fluorescent proteins are you referring to?

Please provide the name of the fluorescent protein and their excitation and emission properties. In Axioscope 2 plus, you can put minimum of 4 filters besides the white light.

Please provide the name of the fluorescent protein and their excitation and emission properties. 

If you have access to an iOS device (iPad or iPhone) you can download the Zeiss Light Lab App. It explains in detail the fluorescent properties of fluorophores and filters. 

http://www.zeiss.com/microscopy/en_us/products/microscope-software/light-lab.html#introduction

CFP/YFP or YFP/RFP would be a good recommendation that provides enough spectral separation between the two colors (even if they have very different expression levels) and has advantages of (1) ability to add a third color down the line, (2) compatible with standard filter sets and excitation sources and (3) availability of many different, good fluorescent proteins (good = bright, photostable, fast-maturing, monomeric) shown to work in many different organisms. Avoid CFP for low expression levels because of generally high fluorescent background at shorter wavelengths. Check out the attached link for an up-to-date database of the best fluorescent protein variants, but keep in mind that it might be better to use a fluorescent protein that's proven to work in your organism or fused to some protein you're interested in rather than the latest and greatest ... it's not totally uncommon that new fluorescent proteins will be reported that are much improved by some criteria, but have weaknesses that aren't yet known.

http://nic.ucsf.edu/FPvisualization/

Thanks for all your answers. My Axioscope 2 Plus has a filter set 09 from zeiss. It allows to use GFP. Since my budget is limited I´ve been thinking to use GFP and BFP and buy the filter set 02 to detect BFP. I can't use RFP since I think chlororplast in leaves will show red fluorescence and I won't distinguish them vs bacteria, neither YFP because my default filter set can't detect it and those which can are very expensive. Am I doing right? 

Your logic makes sense; I don't work with plant tissue, but it looks like chlorophyll emission becomes problematic above ~650 nm (see linked papers). So if you do use RFP, you would want to choose an emission filter that cuts off at or before this wavelength to minimize autofluorescent background.

http://www.sciencedirect.com/science/article/pii/S1369526605001342

http://www.plantmethods.com/content/10/1/22/#B37