When you make a deb package you will need to create several files. The files tend to be kept in a folder called "debian" located inside the folder that configure and make files are in for the package you are creating. Inside the debian folder there should be several files. One is your called "control" This file specifies dependencies of the package that you are creating. These dependencies will be installed if you apt-get to install the package. If you use application manager and dpkg -i to install a package you can then run the command: apt-get -f install to install all of the dependencies which aren't already installed.

Note, you'll also need several other files in the debian folder including a changelog file which will specify the version number of the package and a rules file which will specify how any options when configuring the package.

I always found this thread useful when building debs: http://ubuntuforums.org/showthread.php?t=51003

When a package is depended on, it won't matter what repository that package is in, as long as you have that repository listed in your /etc/apt/sources.list file. If none of the repositories that you have in your sources.list file have a package, then that package won't be installable. But, as long as you have a package and all of it's dependencies (and it's dependencies dependencies..etc) are satisfied you should be able to install it.