I'm doing BE in computer engineering and this is my last semester. Currently I'm doing intern in a company and my final report presentation is in next week. Can I continue working in that company or this will give some negitivity to my status. I will be applying for my OPT card once I pass my presentation.

Not only can you continue your internship following your graduation, you can even extend your OPT for additional 17 months since your degree qualfies under STEM degrees.

For more info, check this out. http://www.uscis.gov/portal/site/uscis/menuitem.5af9bb95919f35e66f614176543f6d1a/?vgnextoid=9a3d3dd87aa19110VgnVCM1000004718190aRCRD&vgnextchannel=68439c7755cb9010VgnVCM10000045f3d6a1RCRD

Do I have to wait for OPT approval and OPT card to continue working in current interning company or I can continue working there even after passing internship period without OPT approval.

 Looks like you're doing internship as a CPT and not OPT. If that's the case, the answer is NO. Once the duration of CPT (stated on your I-20 you got before starting internship) expires, you cannot continue to work. If you continue working, it'll be considered working illegally - just like working at a mall/gas station. If you are doing the internship just like working anywhere else (i.e. without going through the CPT approval process), it's already illegal and working for a few more weeks/months shouldn't do much more harm, if any.

Regardless of when your internship ends, apply for OPT exactly 3 months before you graduate, when applying put the day after your graduation date as your OPT start date, get hired at the company as soon as you graduate, start working without any trouble. 

Lawfully, you can't work without an EAD (be it in the form of OPT/CPT or Economic Hardship) but as long as your employers don't care and ask for it, you don't need to worry about it. And even if they were to ask for it, you could probably show them your receipt. 

I heard if you are doing the CPT for more than a year or something, it would effect the OPT in the long run.. so better know the info about the CPT coz you don't want to screw up in the long run by not telling employer or the school.

I'm not doing CPT. I 'm doing intern instead of final year theiss/research.