I just had a question about integrating ASP.NET into SharePoint. I don't mean to continue beating the subject since there are a lot of posts/sites talking about it, however I am still unsure about the way I am integrating my custom applications into SharePoint.
I had just created my first custom application that communicates with the SQL Database and provides and nice interface for the end user. However the way I published my application is by publishing it under my SharePoint Server such as: https:///myapp/default.aspx. I understand that this way can't use the master page (I been reading that this might not be completely true, but I don't use it anyways) and the only resemblance of it being in SharePoint is that its under the URL (So not really in, but under SharePoint). So now if I log into that server and open up IIS, drill down into that site, I see my application resides under and no problems and I can visit that site and use the app.
OK, lets fast forward a few months into the future. If I begin creating a few more applications and publishing them this way, will I run into any issues?
My Questions: Can I only publish a specific amount of applications to a particular site? Which app pool to use when publishing custom apps?