Download the MS SQL Release files zip and the MySql data layer zip.
Extract both files, copy the dlls from the MySql data layer into the Web/bin folder of the mssql release files
now your release packages is configured for MySql
If you don't already have a user.config file, create one as discussed here and put your connection string there as well as any other things you have customized in the appSettings section of Web.config. This way you won't lose your customizations, because mojoportal does include a new Web.config which will over-write your current one, but it does not include a user.config so by keeping your customizations there you won't lose them. You should at mimimum backup your Web.config file before an upgrade so that you can retrieve any customizations. For example, only appSettings can go in user.config so for smtp saettings you also have to maintain custom settings in the system.net mailsettings section of Web.config so back up your original to get that and put it in the new Web.config
Its best to sign in to your site as admin before you begin uploading new files.
You do want all your mojoportal files to be overwritten. Other than image files you have uploaded, all the content for your site is in the db so nothing will be lost by files being overwritten. Only mojoportal files are in the package so its not going to overwrite any image files you uploaded.
If you customized a skin, you should make sure it has a custom name (ie change the folder name from the original name as included with mojoportal) so it doesn't get overwritten.
Upload the files in steps as dicussed here: http://www.mojoportal.com/uploadingfilestoahostedserver.aspx
After all the files are uploaded visit yoursiteroot/Setup/Default.aspx to run the db upgrade scripts.
If your site is in production use and is mission critical, I recommend doing a full db backup and backup of all web files first so you have the possibility to restore it if anything goes wrong. I don't expect you to have problems but its good to be safe.
Hope it helps,