Wendy we were in a similar situation when DS started eating "our" food - we always ate meals together but at least twice per week there was a ready meal (ie/ supermarket lasagne or shepherd's pie to stick in the oven) as we were both working and home late, lots of whatever we can make quick, etc. I have really worked on things this past year, and by no means am as good as I would like to be but we are doing much much better. Helps that I am home FT with DS and have the time (sort of) to cook, I know.
I have a food pyramid servings listing on the fridge. Just a little handwritten chart with the number of F&V, grains, dairy and meats that we each need in a day. I leave DH to himself and I only pay half attention to my own, in all honesty but I do try very hard with DS and I'd say he is getting his proper amounts each day (though yes, nutritionally balanced I look at a whole week not a day).
For the other things you've said, vitamins, iron, omegas, probiotics, etc, I sat and read a dozen articles on what kids need in their diet (you would be surprised at the variation from one "expert" to another so I read enough until I had a comfortable idea in my mind of either a reasonable compromise between the amounts or went with the sources that I felt most reputable). I did a little check on what the staples are in DS's diet to see what he lacks in - for instance, I know that vitamin C is not something he lacks with how much fruit he eats so there's no concern there and I can not worry. The other foods, I decided what's most important and choose ONE to work on. So for a long time it was fat...DS just did not have enough fat in his diet (hardly any in fact) and we needed to find ways to increase it. I wrote out some extra ways, fattier food choices for him, etc and stuck it to the fridge. Once it got to be more of a habit for me, we moved on to something else...iron. I know my DS gets such little iron and really needs it so I have a little paper on the fridge with how much iron he needs in a day and some of the things he will eat that have good iron levels and how much iron they contain, so I can mentally keep my eye on it. One that gets to be habit we will move on to another one.
I find that when you're looking for the healthiest foods and best choices a lot of the same foods crop up again and again and overlap categories. So if you're looking to boost omega fatty acids and choose to have sardines once a week, you realise that it does the trick for calcium levels as well, iyswim.
But to me it is overwhelming to do everything at once, so I pick little bits at a time. My kid can survive without probiotics but he can't survive without iron (IMO) so I am going to pick the one that is more crucial and work on it first before I stress myself out with the other things.