Best colors for a new build/case?

When looking your MoBo color theme, you're probably looking for black/red themed PC case. There are plenty of such options though, e.g:
Corsair SPEC Alpha (black/red), Corsair SPEC Omega, Corsair SPEC-04, Phanteks P400S TG,
pcpp: https://pcpartpicker.com/products/compare/6Vwqqs,Kg4NnQ,2tTrxr,d4ndnQ/
Also almost all NZXT lineup, specs: https://www.nzxt.com/categories/cases/?color=red

Since S340 comes with 2x 120mm fans (top and rear), front is left unpopulated. To match your black/red theme, i'd go with Corsair ML Pro red LED fans with following setup:
front - 2x Corsair ML140 Pro red LED
top - 1x Corsair ML140 Pro red LED
rear - 1x Corsair ML120 Pro red LED
specs 140mm: https://www.corsair.com/us/en/LED-Color/Fan-Size/Package-Quantity/ml-pro-led-config/p/CO-9050047-WW
specs 120mm: https://www.corsair.com/us/en/LED-Color/Fan-Size/Package-Quantity/ml-pro-led-config/p/CO-9050042-WW
pcpp: https://pcpartpicker.com/products/compare/MpBrxr,sYNypg/
review of 140mm: http://thermalbench.com/2016/07/29/corsair-ml140-pro-140-mm-fan/

In my Skylake and Haswell PCs, i too have Corsair ML pro LED fans in use, both 140mm and 120mm. And due to the build's theme, i have red LED ones in Skylake and blue LED ones in Haswell.
Performance wise, Corsair ML Pro series fans have great airflow (97 CFM for 140mm, 75 CFM for 120mm) with solid static pressure (3.0 mmH2O for 140mm, 4.2 mmH2O for 120mm) complimented with huge RPM range (400-2000 for 140mm, 400-2400 for 120mm) with PWM control (4-pin) and mag-lev bearing. While Corsair ML Pro fans output 37 dB(A) at max speeds, i'm running my Corsair ML Pro fans at about 800 - 1100 RPM and i can hardly hear them.

Cooler Master MasterBox Lite 3.1 and it's bigger version: MasterBox Lite 5 RGB are one of the worst cases when it comes to the airflow. No bottom intakes, no top exhausts, completely solid front panel and support for only 120mm fans make those fancy looking cases wreck havoc on airflow.

MasterBox Lite 3.1 can only support 3x 120mm fans: 2x at front and 1x at rear,
specs: http://www.coolermaster.com/case/mini-tower/masterbox-lite-3-1/

While your MoBo has 1x CPU_FAN header and 2x SYS_FAN headers, using Y-splitters, you can connect 2x fans to single fan header, making the MoBo fan support to 6x fans,
specs: https://www.msi.com/Motherboard/B350M-GAMING-PRO/Specification

Though, to get any decent airflow in that case, i'm not sure if even 120mm Noctua industrial 3000 RPM fans would be enough,
airflow - 110 CFM
static pressure - 7.63 mmH2O
specs: https://noctua.at/en/products/product-line-industrial/nf-f12-industrialppc-3000-pwm/specification
pcpp: https://pcpartpicker.com/product/Mb4gXL/noctua-case-fan-nff12industrialppc3000pwm

If Noctua fans won't cut it, you're only left to go with Delta industrial fans since they are the best there is, e.g Delta AFB1212GHE-CF00,
airflow - 241 CFM
static pressure - 1.082 mmH2O
specs: https://www.digikey.com/product-detail/en/delta-electronics/AFB1212GHE-CF00/603-1325-ND/2560449
pcpp: https://pcpartpicker.com/product/dnPfrH/delta-electronics-case-fan-afb1212ghecf00

But that much i can say that if you want to have any decent airflow in MasterBox Lite 3.1 case, say goodbye to the silent PC since it isn't happening. You can't have good airflow with quiet operation in that case at the same time. Either you have silent PC with no airflow whatsoever or good airflow with 40 - 60 dB(A) from fans. That's how bad of a case it is when it comes to the airflow.
It's sad to see that the latest trend in PC cases is solid front panel with high focus on the looks where the thing that matters - airflow, is disregarded.

The trick to get silent operation with good airflow is to have as much fans inside the case as possible. Since the more fans you have inside the case, the less each fan has to work to maintain the airflow and the less noise fans produce.

For the 3rd time i'll take my own PCs as an example here:
Both of my main builds, Skylake and Haswell, sit in a full-tower ATX cases. One of the reason why i have full-tower ATX cases is due to the high amount of fans they can hold. And i've populated all fan mounting locations with high-performance fans as well, with mostly 140mm fans, except bottom intake fan which is 120mm. While i can also put in 120mm fans all around, 140mm fan moves more air than 120mm fan and it does that much quietly.
And that is also a main reason why i have 7 case fans in my Skylake and Haswell builds (6x 140mm and 1x 120mm). Since i have that many case fans, i can keep all of my case fans spinning between 800 - 1100 RPM and thanks to this, my PCs are very quiet while still having proper airflow inside my full-tower ATX cases.