Is this sentence correct?

i do the adjustments, like changing the color, shape, and any parts of the design

oh, and what is the meaning of "[with-> in, different-> multiple?]" ?

Depending on context, the phrasing might be different. I was just offering possible substitutions.
That is to say:
Each color available with different layers! could perhaps be better phrased as Each color available in multiple layers!

it's the currect phrase,but is just my opinion maybe i'm wrong,i'm not perfect lol

can you explain why the first sentence is not using on?

Generally "in" is more possessive-associative, while "on" is generally more relative-associative. Technically there are exceptions- "on notebook paper, in my binder" should theoretically match to "in PDF format, on my computer", but clearly has the formatting switched.

To explain the latter ("in PDF format, on my computer") structure: Being in PDF format indicates that it's posessive to that format, meaning it can't easily be transitioned out of it- ergo, indicating more of a posessive/linked association. Whereas saying "on my computer" or "on my website" indicates that it could perhaps be presented on another computer or website- ergo, indicating more of a relative/temporary association.

The explaination for the other formatting ("on notebook paper, in my binder") gets a bit more peculiar: In this case, "in" simply means "inside", and therefore avoids the more meaningful associative connotations entirely*. The "on" retains its relative use, as the indication is that the text or artwork on the paper could theoretically be presented elsewhere (for example, being redrawn or scanned into a computer).

* That is to say, it's the subtle difference between "can I have this in blue" and "can I have this in[side of] a blue box". It's clear in the latter statement that the item in question is not inherently associated with the blue box, but is associated with being blue itself with the first statement. You wouldn't use "on" for the box, as that would indicate your placing the item on top of the box, rather than inside of it. In summary, the in/on formatting you'd use changes depending on if you're referring to the nature of the object [eg, in PDF format or in blue coloration, on a computer or on a website], or whether you're referring to its physical location [in or on top of a box].

Again, that's more of a peculiarity. of context. For the kind of topic that is in discussion, it's generally reliable to go with "in" for formats and "on" for mediums for presentation, as per the previous example.

and is it important to add "may"?

Yes. In addition to potenitally making the sentence just sound "off", excluding such phrasing in English can also potentially make your phrasing come across as overly forceful or insistant- which'd give a rude or scammy impression. When in doubt over what phrasing'd cause offense, in English you should rely on using soft modifying terms [in this case, "may"; More broadly, the use of words like "may" or "can" should be used in place of words like "will" or "must" or in place of a lack of any modifying terms at all] and non-personal terms [ie, avoid "you" where possible, if making general statements].

Available on means it is accessible on a platform or carrier media. Available on CD, DVD. Available on Xbox, PlayStation. It is the thing that carries the thing.
Available in means the format of the thing that can be used. Available in widescreen or letterbox format. Available in MP3 or FLAC. Available in red or blue.

So:

• Available in various formats: .AI, .EPS, .PDF, or any other, as requested.
• Each color is stored on different layers. | Separate layers are used for each color.
• Adjustments can be made. | The images can be adjusted upon request. | The image can be customized upon request.

(Side note: You managed to surprise me, based on the phrasing and style I would have guessed you are from Latin America, not the SEA region. I guess I am a bit out of practice.)

• Well, Sooth nailed the explanation of the first point much better than I could've, so I'll point you to that.
• For the second sentence, that's a bit tougher, since I've never used either of those programs. That said, I checked out Aydaylin's link below, and I'm wondering if this point is even necessary, since it's something that most people probably don't know about, and something that color printers do automatically.
• In that case, I'd say "Custom orders available", but that would also imply that there's a default format, and some might think that the customization would cost extra money, which could be a turn-off to some. Without including this point, it might sound more to the customer like they have a lot more freedom with their designs.

I hate to be that gal, but I'm wondering if this bullet-point format of advertising might not be a good fit for this. You might want to consider just a flat description of the service you're providing, or have the bullet points just be the different kinds of options that are available. For example, available formats, available colors (if relevant), available graphics (if you have any shapes or anything you can add to it), how many bits of text can be put into a single work. That kind of thing is much more informational, and while it might be a bit less exciting and eye-grabbing, it is a very no-nonsense way to let prospective customers know what they're getting, and I, personally, would appreciate something like that.

Thanks for explanation :) Another noob question incoming: what is the advatage of these layered colors?