Milos,
The "Fs," command is a little confusing. IF you do "fs," you need to include the number of ships from each of your ship designs that you are going to send, whether they actually are at the planet or not. The order of these designs is shown in the "fleet," command. You need to occasionally put 0s in. So it's something like "FS 15 5 0 0 0 5", depending on the order.
At the start of the game you only have a colony ship and two scouts, but you have designs for a basic fighter and bomber, which are taking up space in the design list and will always be 0. So I recommend scrapping those as soon as you can and replacing them with something better. You will only ever have up to 6 designs in production at any time. Furthermore, if you just want to send the first design in the list, you can just use one number and omit the rest. It only becomes tricky when ou have different designs, or want to send one of the ones on the far end or whatever.
As a shortcut, you can just do "fs system," to send all the ships in one system to another, regardless of their design.
To answer your other question, you can use "Fs," commands, or the "Rloc," command, to send ships that are built on one world to another one. I recommend not spreading out over too many systems because it becomes hard to manage.
Your question about missile bases is a good one. If you can research better armor and shield tech, you can ignore missile hits. Shields in particular will just ignore damage below a certain point. I also recommend bombarding the planet from orbit if you can, which will destroy bases each turn.
Hope this helps.