Modified oligos should be stored at -20°C in the lypholized state for long term storage. Most modified oligos can be resuspended in TE buffer or RNase free water. We recommend making a stock solution then smaller working aliquots. By making aliquots, you prevent repeated freeze/thaw cycles that can lead to degradation of the oligo.
For light sensitive dyes, you will want to store them in dark tubes or wrap them in foil.