I just wanted to understand your needs when you say you need to manage two email lists, from Mailchimp and paper.li...
If you decide to use Mailchimp, we normally recommend that you remove the Paper.li subscription box and replace it with a mailchimp one. That way, the export of subscribers to Mailchimp is a one-time-only deal. :) . After you export Paper.li subscribers, you can hide the paper.li subscription box and insert one from Mailchimp. That way, you won't have two mailing lists.
Copied and pasted from Support article:
For Mailchimp, click "Mailchimp" and follow the steps shown:
STEPS ONE, TWO, THREE are only done the first time you set up Mailchimp.
STEP ONE: Show a mailchimp subscription box on your paper, rather than the default paper.li subscription box. Turn on the toggle and follow the link shown to get the code for your Mailchimp subscription box. Once you've installed the Mailchimp subscription box code, your Paper.li subscription box will not be shown.
STEP TWO: Assuming you will no longer be collecting subscribers using paper.li subscription box, you can export your already exisiting subscribers to either an existing Mailchimp list or a new Mailchimp list.
STEP THREE: Delete your paper.li subscribers, if you no longer wish to use Paper.li to send your newsletters for each edition. If you skip this step, your Paper.li subscribers will also get a Newsletter from our service.
STEP FOUR is done for each edition you send. Step FOUR is quick and simple but not automatic.
STEP FOUR: Click Export Newsletter to Mailchimp to fill in fields for your Mailchimp Campaign. Once you click "Export to Mailchimp", sign into Mailchimp and send your campaign.
Would this process work for you?