We are investigating expanding the IDE's GUI Flash Programmer to support non-LinkServer debug probes in a future release. But in the immediate future, you have two possible ways forward - assuming your FRDM-K66 board has J-Link firmware programmed into its OpenSDA built in debug probe.
1) Replace the J-Link firmware with CMSIS-DAP (DAP-Link) firmware from : http://www.nxp.com/opensda. You will then be able to use the MCUXpresso IDE's built-in GUI Flash Programmer (as described in the MCUXpresso IDE User Guide).
2) Use the tools provided by SEGGER themselves to program flash. MCUXpresso IDE installs a version of the SEGGER software onto your PC and you can download and install the latest from SEGGER's website. For instance you can use the JLink executable (aka JLink Commander) with the "-CommandScript" to program flash from the command line (see section 3.2.3," Using command files" In the SEGGER J-Link User Guide for an example of this). And the "J-Link control panel" offers a way of doing this via a GUI interface.
3) The above two options should also be possible if you use an external debug probe too, such as an ~$20 LPC-Link2, which may give better programming speeds if this is something you are likely to do often (as well as improving debug performance).
Secondly, with respect to your comment "I power off the board and power back on the device will not run" this could be related to you creating/importing your project with Semihosting enabled to provide printf support via the debugger console(which requires a debugger connection to run).
One of the new features added in MCUXpresso IDE v10.1 was to provide a hard fault handler in projects which would allow them to execute even with no debugger in place. Please see the MCUXpresso IDE v10.1 User Guide for more details on this (for instance section13.4.1, "What is Semihosting?" and also section 10.3.1).
The other approach would be to create your projects with UART selected as the debug console mechanism rather than semihosting.
Regards,
MCUXpresso IDE Support