If you don't know if you are replacing a tube on the channel you are plugging into then remove the tube. No harm will come to your amp. If you still get sound then the tube is not in the circuit. Skip replacing such a tube, instead consider it a spare tube holder. Do replace the tube back to its socket. If you don't want to pull that tube then turn up one channel, turn down the other and plug your guitar in. When you tap gently on a tube with your fingernail or an eraser tip then you will be able to hear what tubes are in that channel by the presence of your tapping on the output of the amp. The tube that taps most loudly is the gain tube.
You can identify microphonic tubes by tapping them as described above. Consider that since all tubes have a mechanical construction that they all possess microphonic characteristics to some degree. Microphonic tubes are problematic only if they are causing changes in the amp sound while playing. So to tell if the tone you hear when you tap is really a problem you must first be hearing something is wrong with the amp, and then you can nail down which tube it is by turning the amp up a bit and if your tapping results in a sound that sustains itself then BINGO. Substitute the tube without changing your amp settings (except power it off) and then retest.
Example On refining your amps sound - for some Marshall players, some MetaL forms. You know your amp well. You play a rapid fire style that is percussive and you find the tone nice and clear but too razory in the treble zone. For the GAIN stage you will most of all need an accurate tube to articulate that speed and percussive quality without getting squishy. Then as a secondary concern you want to tame that treble, so your FUNCTION tube should sound warm.
What if you want balanced tone - dark driven beefy cream? Okay. "Warm with mild COMPRESSION and early distortion" GAIN tube, perfected with "Clean and COMPRESSED" to get the complete attitude. Rock on. Almost but not quite? Switch the 2 tubes...give another listen (you will need each tube to be Applications Graded™ for "GAIN" performance in order to swap). This is FUN!
For a great clean sound start with what you think your amp is lacking, and or what its needs more of.
Ex: I need to play louder without the amp breaking up where there is bass. I like to be loud and clean, try the "clean and accurate" tube in the gain position, and make sure you have a good working DRIVER tube (a potential source for clipping specially at louder settings). That selection of a gain tube will help to keep the bass tight and never add distortion to a clean channel. The driver needs to be a driver. Its can be anything that is not dark or easily distorted. Of course its tonal qualities further refine the amps response but not in a critical manner.
