There is more than one way to start a supplement company. There can potentially be a lot of steps involved, but none of them are difficult to implement. In a nutshell, here is how you do it.
1.) Name your company: This speaks for itself.
2.) Figure out what you want to make and name your product(s): This may need to be re-evaluated once you start working with a manufacturer, as production costs will ultimately determine what you are able to do. You also have to evaluate the market in order to determine if your product is a viable seller (just because you want to make something, it doesn't mean other people will want to buy it). In short, your product must be cost-effective and meet market demand.
3.) Find a manufacturer: Once you do this, the manufacturer will be able to tell you what compounds are available to you and what their costs are.
4.) Find a label company: This step requires nothing more than a phone call. Once you've selected a company, you can go about getting labels made in one of two ways. You can either design the label yourself and have the company print them, or you can have the label company design and print them (there is an additional, hourly rate for label design). You can have as little or as much input in the design process as you like.
5.) Determine bottle size/type, label size, and whether or not you will be using capsules or tablets (capsules are almost always cheaper and equally effective): The manufacturer can help you with this process, as he/she will likely be thoroughly familiar with what size label you will need for which size bottle, etc. Once you have this information, replay it to the label company so they know what dimensions your labels need to be. Once labels are complete, the label company will ship them to the manufacturer and the manufacturer will put them on the bottles.
6.) Get a business license: This will cost you around 50 dollars and will take about one day to do.
7.) Get a merchant account: You can walk into any bank and they can walk you through this process. You will need good credit in order to get a merchant account. Some people choose to bypass a merchant account and open a business account through Paypal, which will allow you to accept all major credit cards, as well as accept payments through standard Paypal services. Keep in mind that Paypal will report your earnings to the IRS once you surpass 20K in total sales.
8.) Have a website and company logo designed: There is a multitude of experienced website designers out there who are more than willing to do this type of work for you.
9.) Set-up a Business Facebook page: You can either do this yourself, or have someone do it for you who is experienced with this.
10.) Set-up an encrypted e-mail account: This will allow you to safely and securely receive and store customer order information.
11.) Determine your ideal target demographic and distribution route(s): Are you going to focus on online sales and the wholesale (retail store) side of the business. If selling online, you need to figure out which you best advertising route is for the products you will be selling (i.e. sponsorships, etc).
12.) Determine how you want to ship your products: In most cases the manufacturer will ship your products for a low cost (shipping cost + small additional profit), or you can do it yourself via USPS, Fed-Ex, etc.
These steps are not necessarily in the proper order and there are a lot of other details you will need to concern yourself with as you go through the process of starting up your own supplement company. Of course, you will also need a decent sum of money already set aside in order to pay for raws, labels, bottles, website, bank fees, etc, etc, etc. Depending on what you are doing, you could probably start up a 1-2 product company for between 10-15k, but again, it all depends on what you are going to make, where and how you are going to advertise, etc.
Furthermore, not all compounds can be purchased in the same quantities and prices can vary dramatically. For example, making a BCAA product would be dirt cheap as basically every manufacturer already has BCAA's on hand and their cost is low, but if raws need to be ordered from a compounding pharmacy costs can shoot up quick because minimum orders are often required. So, if you get stuck having to buy a kilogram of a certain compound and it costs 16k per kg, that means you would need to pay 16k just for that one compound, even though you may only need a fraction of that amount in order to make a several hundred bottle run.
You usually won't get stuck having to make a purchase that big for a single compound, but trust me, costs can go up quick when dealing with multi-compound products in the upper-price range.