First, yes do drain whatever fluid is in the strainer via the drain on its bottom. Make sure to put the plug back in after you drain the strainer.

Second, with the strainer seacock closed, open the drain plug on the side of the seacock. That will drain out any fluid in the ball valve. Make sure to replace the drain plug and leave the seacock closed. You should do this for all seaocks you will leave closed. If there is a hose between the seacock and the strainer, pull it off the seacock and drain any water from it then replace it. This is a good time to chck the condition of the hose and the clamps holding it to the strainer and seacock.

As far as your electrical system is concerned I would do the following if it hasn't already been done. Connect a battery combiner relay between the start and house batteries. That will combine your batteries whenever there is a charging source (alternator, charger, solar panel). Connect the solar panel to the one battery. That way when the sun is out it will pull that battery up and cause the battery combiner relay to connect the two batteries for charging. You never have to move any switches to charge. As far as alternator charging goes, once you have a battery combiner between the two batteries, connect your alternator output to the start battery. The combiner will automatically parallel the two batteries when the engine is running. You do not have to remember to set switches any particular way to charge your batteries.