the metal tubes can be very sensetive little things. they may look like they are in good condition but even a slight warpage will casue a leake or popping out. if they seem perfect go ahead try reusing them. yes replace the seals in the valve cover and replace the valve cover gasket while its off. and replace teh cam position sensor while the vc is off as well its easier that way trust me.
now to seal the tubes you can absolutly use a gasket marker. the problem wioth that is that it is an anabolic sealant meaning it never truly dries and requies oxygen to do do so. no much in the head. it is best to clean teh end of teh tube with either fine grit sandpaper or scotch bright then wipe it clean and use a little bit of red lock tight. the tubes do not need or like to be pounded into place they bend. put on a pair of gloves or rag and line them up and push hard. they all go in level and seat witha bit of force. no hammers dead blows mallets just hands. then you have a well working tube.