I'm using a fluorescence plate reader to titrate FITC and TRITC. Should I set the plate reader to read at the excitation and emission levels for each of the fluorophores?
Yes. Fluorescein and tetramethylrhodamine have different excitation and emission maxima. If you want to get the most sensitivity, you should set the plate reader excitation and emission wavelengths to different values for the two dyes. Typical settings for fluorescein are 485/520 and for tetramethylrhodamine 540/590. However, if sensitivity is not an issue because the fluorophore concentration is high, you can measure with the "wrong" wavelengths.