I'm not sure, but it sounds as if you might be getting confused by conflicting conditions.
Try thinking of it this way.
Let's say you have two conditions, and two formats you want to apply.
Condition 1
If A1>A2, make text red on a yellow background
Condition 2
If A1>100, make text blue on a green background.
Let's say your default format is black text on a white background.
There are then four possible outcomes -
Outcome 1, A1=1, A2=2, Condition 1 is false, Condition 2 is false, Excel will apply the default format, black text on a white background.
Outcome 2, A1=2, A2=1, Condition 1 is true, Condition 2 is false, Excel will make text red on a yellow background.
Outcome 3, A1=101, A2=102, Condition 1 is false, Condition 2 is true, Excel will make text blue on a green background.
Outcome 4, A1=102, A2=101, Condition 1 is true AND Condition 2 is true.
Excel will base its formating on whichever true condition comes first.
In this case, it will apply the formating for Condition 1 and give you red text on a yellow background. If you reverse the order of the Conditions, it will give you blue text on a black background.
What you need to do now, is think about all the different ways that your conditions could be true / not true, and then build your conditional formating to reflect that.
It is usually simplest if your conditions do not overlap, i.e. only one can be true at a time.
If it is possible for several conditions to be true at a time, you can use Conditional Formating to reflect this, but you need to be more careful about how you set it up. One way to help you do this is probably to take the set of circumstances that relate to two or more conditions being true, and make that your highest priority condition.