QB Issue Resolution:

yes, each company is its own subscription

see this for a comparison so you know whether the functions you rely on in desktop are in QBO or not

a non partisan comparison of QBO vs QB desktop
http://onsale-apparel.com/Rustler/qbo-or-qbdt

Resolution for Issue 'I currently use QB Pro 2013 (desktop) for two companies which has records starting in 1994. I want to move to QB Online – do I have to get two separate online accounts?' available: Yes (Solved).
Source: Intuit Community forum.

I currently use QB Pro 2013 (desktop) for two companies which has records starting in 1994. I want to move to QB Online – do I have to get two separate online accounts?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Desktop
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Error Recovery for Desktop [Canada]
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