Having the combination of new pieces and old pieces will not affect handling.
Your car should feel better when you put the new ones in the back though, because the stock pieces should have deteriorated somewhat.
The isolators are there just to dampen road noise and make your car feel better.
Some people don't use isolators, which lowers the car about 3/8 of an inch (give or take a little)... I am guessing that the vehicle would handle slightly better around turns since it is slightly lower, but the difference will most likely be difficult to notice.
I am doing my suspension and I purchased Energy Suspension pieces.
Sooooooooo you have nothing to worry about... good luck... what manufacturer did you go with? I was going to go with the stock rubber, but decided on some urethane stuff for durability.