If you are using Meade filters, you will need to image through a colour filter and the IR filter at the same time due to their spectral response. If you want to be parfocal, put all your Meade filters in the wheel and the Baader filter in the nose piece, effectively imaging through 2 IR filters or 1 colour and IR at the same time as stated before. Also, with the DSI Pro, you will need at least an IR filter, you cant use them too well with out. A clear filter is not recommended due to very quick pixel saturation by bright stars in your image field. I run mine this way for the same reasons you ask. Have had no problems.
