My main drain go to a 90 but it's four way with two screw caps will this cause back ups but it's been there 20 years backed up little before but now all time

Direction of cleanout or number of cleanouts will NOT contribute to a blockage...will only aid you in snaking the drain..;) Remove the cleanout caps and fill the drain to overflowing and then rent an electric cable machine from a local tool rental store (and get goggles and leather gloves) and snake the drain clear!