Is there any way I can check that I have done all the side quests?
Hello there Silver Misty Trice
Although there is not yet an in-game checklist where you can see which quests you have and have not completed, there are internet sites that have lists of side quests for each world. The pirate101 wiki on the centralforums site has lists of side quests (although Marleybone and Aquila have not been added as of yet). You can select those two worlds and sort through the quests that way though.
You can go to click on each world individually under the quests by world topic. This will bring up the quests for that world which you can then select the quest and it will tell you whether it is a storyline or side quest. This can be tedious however- going through each quest individually.
Just click on the quests tab and you can search the various subtopics. There is a lot of useful info on various topics as well, so have fun exploring. There may also be other posts listing side quests on pirate101 centralforums and the many other fan websites. You can do a search and see what you come up with.
In Aquila it pays to go back and check out those islands that you have finished main quests on. I docked at one by mistake once and was startled to see a quest waiting there for me. More than one has quests that show up later that are side ones that you will not need to finish the story. So do a little sightseeing and revisit those places and have another look-see.