It's possible we'll have a batch tool to modify subscriptions in mass in the future, but there's no plans at this time. For the manual renewing subscriptions you can use the below query to increment their expiration dates to extend their subscriptions. Be sure to make a backup of your database before doing this just to be safe.
Code:
UPDATE `jos_cbsubs_subscriptions` SET `expiry_date` = DATE_ADD( `expiry_date`, INTERVAL 3 MONTH ) WHERE `status` = 'A' AND `plan_id` = PLAN_ID_HERE AND `autorecurring_type` = 0
Replace PLAN_ID_HERE with the actual ID of your plan. The autorecurring type check will cause this to only apply to manually renewing subscriptions. It will also only apply to already active subscriptions. This should add 3 months to their expiration date. I've tested this locally to be sure it functions to be safe and have confirmed it works.
There's nothing you can do about auto recurring subscriptions except cancel them. We've no functionality to pause subscriptions and most gateways have no such functionality. You could extend their subscription dates, but that won't stop them from being billed on the next renewal.