Which incubator is it? Make and model? Or do you have a link that shows details? It helps to know what you are working with.
doesn’t have the best option for humidity. Its just a tray over the bottom of the incubator where the eggs sit and under there you can put water.
That's a standard system. What determines humidity is water surface area, not depth of water. The more area that moisture can evaporate from the higher the humidity. Mine has four different trays of different sizes. I manage humidity by which trays I fill with water. There are some tricks people use to increase humidity. Some people add another tray. Some put a corner of a sponge, paper towel, or cloth in water so it wicks out water and gives more surface area for it to evaporate from. Not knowing what your incubator looks like I don't know which might be appropriate for you.
Another possible problem is that you may be having too much air exchange. One time I did not get the lid back on correctly and the humidity dropped significantly. How many vents does that incubator have? The chicks need a certain amount of fresh air so you probably need one vent open but they may not need two open.
If I fill it up all the way to the top the humidity reads 40. That’s weird to me because the instructions say it has to be 55, but it won’t even allow humidity to get up to that. My chicks have been all growing perfectly fine, I candled them and saw very lively babies moving around. On day 18 I stopped touching them.
Some people get good hatches at 30% humidity, some 40%, and some do best at 50% or over. I found that my sweet spot was 39%. There are a lot of different factors that go into that, it can be different for each of us.
Is the hygrometer calibrated is a good question. Unless you have confirmed it is reading correctly it can be off by a lot. I don't trust the factory presets or instruments that come with the expensive incubators, let alone the inexpensive ones. Your actual humidity could be a long way off from what you are reading.
I made the mistake of putting different eggs in a week later, after I out these ones in. so I have eggs hatching tomorrow and then eggs hatching next week! I didn’t understand that humidity has to be different. I don’t know what to do because it has to rise for the hatching ones, but it’s filled to the top and the others ones are still fine but it’s day 20 and I haven’t gotten any pips from the ones that should be hatching. Hope that’s not too confusing! What do you suggest I do?
That is a very common problem on here, especially for first time hatchers. It is not ideal but raising the humidity for a few days isn't likely to hurt the later eggs. What I'd be more concerned about is that the first chicks that hatch can slime the other eggs and make a mess in the incubator. That can allow bacteria to grow and turn the incubator into a stinky slimy mess which can kill the later chicks, let alone stink up your house. There are solutions.
The simplest but most expensive is get a second incubator and use it as a hatcher. When it is time to lock down the eggs move them to the second incubator. People that do staggered hatches often have two incubators for this purpose.
Depending on what your incubator looks like and how many eggs you have you may be able to put "baskets" over the eggs that hatch first to keep them contained when they hatch. You can fashion baskets out of hardware cloth or perhaps use those little baskets berries comes in, something like that. Or build a fence out of hardware cloth to keep the chicks away from the later eggs. Then clean the incubator when the first hatch is over to prepare for the second hatch.
You can just let it go and see what happens. Sometimes that works.
