advisable to remove the whole roof then it would be easier, but unless you have 'rubber hands' like 535i, you can try changing it when the roof is on tilt and partly slide to the back
Speaking about mobile acquarium...mine became just that coz the drainage hole was stuck on all sides ...so when it rain heavily my car will rain inside also....i clean out the hole and was fine...i did not replace the rubber but it looks easy to replace. According to my friend the rubber is only to block out the wind sound when driving at high speeds.