How to assign string to array columns after split method

The first thing to do is to think about what you are trying to do: rather than creating a 3D array with fixed sizes and getting the user to input the count, consider a List instead, so it can expand as needed:

List<string[]> storeSemesterProfit = new List<string[]>();

Then let the user enter data util he runs out and it's easy to store:

string storeData = Console.ReadLine();
while (!string.IsNullOrWhiteSpace(storeData))
    {
    storeSemesterProfit.Add(storeData.Split(' '));
    storeData = Console.ReadLine();
    }

Even better would be to convert the strings to actual numbers at this point as it's easy to get the user to fix his typos:

List<decimal[]> storeSemesterProfit = new List<decimal[]>();
string storeData = Console.ReadLine();
while (!string.IsNullOrWhiteSpace(storeData))
    {
    string[] parts = storeData.Split(' ');
    decimal[] profits = new decimal[parts.Length];
    bool ok = true;
    for (int i = 0; i < parts.Length; i++)
        {
        decimal value;
        if (!decimal.TryParse(parts[i], out value))
            {
            Console.WriteLine($"{parts[i]} is not a number: line ignored, please reenter");
            ok = false;
            break;
            }
        profits[i] = value;
        }
    if (ok)
        {
        storeSemesterProfit.Add(profits);
        }
    storeData = Console.ReadLine();
    }