You can mix and match mikroE and MPLABX tool chains, but the experience is not as pleasant as sticking to entirely one or the other.
For instance, you can compile with ME then use MPLAB and PICkit3 to debug, but that means switching between IDEs and I suspect (not sure) that less information is available this way.
Debugging ME with the ME programmer is a much more pleasant experience. Debugging on easyPIC board is really nice, since everything is self contained (built-in programmer) and the board is large, making connection easy.
Trouble is the bill for ME ends up huge, because the more you get, the more you want. I have spent many thousands of £
Starter system might be something like:
PIC Compiler - £300
Programmer - £100
EasyPIC7 - £150 (cheaper if bought as a kit with compiler, LCD, GLCD)
a couple of click boards (not vital, just for fun) £60
.... so somewhere around £600 to start off (all prices approximate and from failing memory)
Then you may want:
PIC24 Compiler £300
PIC32 Compiler £300
Then you might be tempted to get more Development boards and more click boards - ends up a lot of money (but IMHO worth every penny)
MCHP toolchain is a lot cheaper if you can live with free versions. Remember XC8 only does 8 bit PIC, so there are two more compilers to buy at £700 a time if you want 16 and 32 bit PICs should code size and speed turn out to be important.
Tried CCS copiler 45 day trial - seems OK, but I can't find a way to use PIC register names in a straight forward way. Guess I am old and set in my ways, but I much prefer a nice standard statement like " LATB = 0x55;" to: the CCS way of "output_b(0x55);". Even if it turns out that there is a way to use real SFR names as in the datasheets, the programs I have seen do it the CCS specific way. Not found any other obvious reason to dislike CCS, but that one issue may be enough for me to not want to explore further.
The other down side of mikroE is that it is so easy and so nice to use that you may get lazy, and struggle to return to other tool chains.
Another issue with mikroE is that libraries are closed source, so if you want something other than the supplied library routines, you end up having to write them yourself.
Sorry for the wordy response, but choice of toolchain is not easy, and before you commit to investing big money, you should be aware of the limitations of each.
Hope this helps, rather than adds confusion