I think that you are trying various adjustments to find which will work for you. I have D3300 and both the lenses you have. Here is what you can try
. "A" - aperture priority
. ISO - 100
. Aperture - F4 to F8. Avoid using higher F stops
. Metering - Matrix
. AF - AFS, that will give a confirmation "Beep" when it is in focus
. Select the Centre for AF, that is most sensitive
. File - RAW
You can ignore the other settings as they can be applied in Capture NX-D when you process RAW files.
Just be aware of a few things
. Regions marginally out of focus will be soft and not tack sharp, any motion blur and camera shake will also result in soft images.
. At F1.8, the DOF is very narrow, so use it only for portraits, for architecture F8 is optimal.
. RAW files are 12 bit, JPG 8 bits, so latitude for recovery of shadows and exposure compensation is much more in RAW. Use jpeg only when you need the space and delivery speed.
. The 18-55 is a reasonably sharp lens at F8.
. 18-55 at 55mm can get you real close and gives a magnification of 0.3+. Use that setting for close ups.
. Inbuilt flash has a guide number of 12, which means at F8 you have only 1.5m of usable range.
. External flash usually have a usable range of 10m or more (depends on the focal length, the longer it is the more range in advanced flash as the beam narrows).
. For indoor shots use external flash with head pointed up. Use matrix metering and if needed Exposure Compensation of +1.
. Spot metering gets the exposure right only around the spot. Any region brighter will be over exposed and darker under exposed.
. The usable ISO for D3200 and D3300 is 400, if you want medium shadows clean.
I hope this can help you.