When you have used the "Group By" right-click menu item on the Peak Areas graph to group the replicates by a replicate annotation such as "Condition", there is no way to change the order that those appear in the Peak Areas graph: the annotation values will always be sorted alphabetically.
If you would prefer them to appear in a different order, we would recommend that you change the names of the conditions (e.g. "1_NF", "2_ICM", "3_NICM").

If you have not grouped the replicates, so you are displaying one bar per replicate, you can use the "Order" right-click menu item to choose different orderings.
If you have chosen "Order > Document", then you can change the ordering of replicates using the "Move Up" and "Move Down" buttons at "Edit > Manage Results".

If you would like to learn about comparing peptide quantities between groups of replicates we would recommend that you look at the Group Comparison tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_grouped
-- Nick

Thank you for the PDF , it was very helpful , also when I try to renitegrate data from refine toolbar it gives me the error that the current peak modeling is incompatible with some of the peptides I added , do you have tutorial on how to change the model in a way that works best for my work ?

Best,
Sogol

Here is the tutorial about training peak picking models:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_peak_picking

If Skyline tells you that the model is not compatible with your document, it means that you have at least one peptide which is missing one of the feature scores that the model uses.
On page 10 of the peak picking tutorial it talks about how to find the peptides with missing feature scores by clicking on the binoculars button below the "Unknown" bar on the feature bar graph.
-- Nick