using wrong 12v connection possible prob?

I work at a business that installs auto starts (i know nothing about installing them, I do other install work) I had one of the other employees install an auto start into my 2005 grand prix and have had nothing but problems with it since, . while he was doing the install i checked in on him and he was hooking up the 12volt(extended using a 10 guage wire) to something behind my heater/ stereo controls ( instead of to the fuse panal like i noticied on the instal sheet) he said it doesnt matter where u hook it up at. the first problem i had was service security system would come up on my dash and my defroster/ heater wouldnt work whenever this happened ( i asked the technician about it and he said the car was going into limp mode and cutting out some options .. so he changed the bypass) my heater and defrost would work fine unless i used the remote start.. my car has been in the shop 5 times now and is still doing the same thing , however the other day (i used the remote start and the service security system came up as usual but this time my heater worked) after a few mins i smelt burning plastic and my heater stopped blowing hot air.. I have since had the coolant system flushed, the heater core flushed separately, changed the thermostat and still no hot air.. funny thing is since the burning smell and the loss of heat my remote start works fine and no service security system message.. but no heat and im on the east coast , canada. Any opinions or theories , ideas anything would be extremely helpful and very much apreciated..

This is what i found on here which is the same as on the install sheet.....

12volts red (50A), red (40A) + back of fuse box, passenger dash