1. Is there anyway to update a package without updating all the accounts in that package?
If you update an existing package, all the accounts that is under that specific package will reset with the new quotas you set. It is better to add another package and to upgrade the desired account(s) to the new package instead of updating the existing package.
2. Is there anyway to update, say, just the feature list of the package for all accounts without updating the quotas etc for all accounts?
Yes, you can use the option Feature Manager in WHM and can edit the feature list.
3. Is there anyway to update per account the features an account is given. For example, if I want to give shell access to a client?
You can use the option "Modify an account" for change features per account. But, please be advised that shell access is not available on a shared server.
4. Also, I'd like to be able to manage quotas so I can allocate more than is being used. It's just much easier to manage this way. I used to be able to do that, but something changed along the way. Can I have it setup this way?
I am not sure which option you are referring to, however you can easily change the quota of any account by listing the account and just by clicking the quota of an account, that will direct you to the quota modification page Main --> Account Functions--> Quota Modification
Also, you can have a look at http://docs.cpanel.net/twiki/bin/view/AllDocumentation/WHMDocs/WebHome for complete WHM documentation.
5. I read in the documentation that there is a way to change the notifications for disk use and bandwidth use. Where can I change this?
I want to change when a notification is sent and I want to change the message.
Please be advised that the disk space/bandwidth usage notification settings are done at root level and it cannot be done by the user. What you have to do is to set a contact email on the control panel of the main account [as of now you set service@domain.com as contact email] and the disk quota/bandwidth/mail quota warnings will send to the cPanel contact email.
As of now, the server is tweaked to send the notifications at;
You can change the notification in the TWEAK setting in the WHM.
