If your suit is styled as you state ("john doe, registered agent, abc.com") it may not be a valid suit.
It is very common for Pro Se (Pro Per) litigants to list the wrong party, or in the wrong style and this could be sufficient enough to throw out the lawsuit, or a default judgment.
In your case, your lawsuit should have been brought against the corporation, in its FULL CORRECT corporate name, with notice served on the registered agent. And if you win (or won), that is the ONLY party that you can collect from.
Q1) "on the warrant it says "john doe, registered agent, abc.com. ", can i still sue the company?"
A1) What do you mean??? Your earlier posts said that you had already sued and won!!!
Q2) "and for what?, the bad checks or a warrant of debt?"
A2) Again, you said you already won!! If so, why are you asking what to sue for??
Q3) "how do i find out if they filed for bankruptcy?,"
A3) Contact the bankruptcy court in the location of their corporate office.
Q4) "what if my boss has bought the business i worked for and is running privately from the parent company, could i sue him then?"
A4) Maybe. If his purchase agreement included all assets and liabities of the corporation, he would be liable.
Sorry, but you seem VERY confused about what you have done and to whom. With all the contradictions in your post, I would suggest you take all your documents to an attorney in your area for his review. He would best be able to sort this mess out and determine what, if any, your next action should be.
Best of luck....