I hope while packaging extension you have included all of your code related to your extension in the package. You might have packaged following files/folders
app/etc/modules/Namespace_Module.xml
app/code/<codePool>/Namespace/Module/etc/*
app/code/<codePool>/Namespace/Module/controllers/*
app/code/<codePool>/Namespace/Module/Block/*
app/code/<codePool>/Namespace/Module/Model/*
app/code/<codePool>/Namespace/Module/Helper/*
May be you have also packaged layout
and template
files present in your theme.
You need to upload only your package [My_Extension_Name]-1.0.0.tgz
to Magento connect https://www.magentocommerce.com/magento-connect