We thought we would generate postive SEO results by putting our links into sudomains off of our main site.So our main site is foo.com and the link to a clinic would then be clinic1.foo.com, clinic2.foo.com, etc.I'm only seeing via google webmaster tools that 2 of our pages are being indexed on foo.com, as we are early on in launching, should we abandon this scheme and go with a more traditional subdirectory URL structure?If you would like to see the live version rather then the example above you can find it via http://bit.ly/1GyyKdT and you can simply click on any clinic. Thanks in advance. 
Individual subdomains for my links
seo
There is not enough information to make a full recommendation, however, I can say this:Make your site for humans and not machines.Any trick or scheme to increase search performance will largely fail.It is far better to create one good site than many lesser sites.Each sub-domain is a site. These will all be related within a single realm by virtue of the fact that they are sub-domains of the parent. Link schemes can be discovered using AI (artificial intelligence) with a long history of pattern recognition as seed data makes pattern matching very trivial. Keyword links to keyword sub-domains should be an easy pattern to detect. Each site has to perform on it's own including sub-domains. If any site does not contain sufficient content, they will be seen as thin and will not rank. As well, the lack of performance for one or more sub-domains will effect the parent site and vice-versa. If a site is new, then ranking will be difficult enough without adding complication into the mix.As far as parameters go, they perform nearly as well as directories normally and can have some advantages over directories. Parameters should be something easily recognized such as user=value, page=value, etc. Each value should be something easily recognizable too. Parameters such as ?x=312&t=202&u=0836728 offers absolutely no value whereas ?page=how-to-fight-referrer-spam&tag=referrer-spam&user=unclefester will. In this way, you can rank moderately well as long as you are not getting carried away.My advice is to remove the sub-domains and simply create one fantastic site.The reality these days is that websites over time have had to compete with a wider array of other websites and through evolution, the natural order of things, websites have gotten better and have become more search efficient. This means the bar is constantly being raised and you have to work harder to compete day by day. There is no substitute for content content content that performs performs performs. No trickery can overcome lack of preparation or short-cut the processes. It is simply impossible to make-up for lack of performance. Any site will have to fight for a period before they can compete with sites that already exists. They paid their dues and so must any new site. It is that simple. It takes time and work to rank.