switching from Atmel studio to Arduino IDE = AvrDude out of Synch

Since i am in the process of trying to learn how to use Atmel studio for my own purposes
I have go back to the Arduino IDE when i want to work on a project
but every single time, and now its just annoying me , the Arduino gives me an

"avrdude: stk500_getsync(): not in sync: resp=0x00"

error.

the only way i get it to work is by burning the bootloader again using my usbTinyISP

I also use the usbTINYISP to upload the sketches or rather the hex file when using Atmel .
I can only upload Sketches from the Arduino IDE using the usbTINY and going to "upLoad with programmer" option
the problem with that is that i lose the ability to use my serial monitor for debugging.
so then i have to burn the bootloader in order to plug the UNo board directly through usb and get my serial monitor back...

any ideas as to why its giving me this error when i try to use the board directly through its usb

well i found a work around, just upload with tinyISP and then plug it in through the regular usb and i can still read my serial print outs through the monitor

If you upload via your usbtiny, it will erase the whole chip (including the bootloader), EVERY TIME.
That's just the way ISP programming works; you can only do partial chip programming (leaving the bootloader intact) THROUGH the bootloader.