Здесь я исправил расположение заданных виджетов (а не их функциональность) в соответствии с заданным вопросом. Вы можете пойти по этому пути, чтобы получить желаемый формат:
from tkinter import *
from tkinter import filedialog
def forButton1():
filename1 = filedialog.askopenfilename()
with open(filename1) as f:
for i in f:
myList.insert(END, i)
print(filename1)
def forButton2():
filename1 = filedialog.askopenfilename()
with open(filename1) as f:
for i in f:
myList.insert(END, i)
print(filename1)
def forButton7():
root.destroy()
root = Tk()
root.title("Spatialization of DSSAT")
root.grid_columnconfigure(0, weight=1)
topFrame = LabelFrame(root, text="Select input file")
topFrame.grid(row=0, column=0, padx=8, pady=8, sticky=N+E+S+W)
topFrame.grid_rowconfigure(0, weight=1)
topFrame.grid_rowconfigure(1, weight=1)
topFrame.grid_columnconfigure(0, weight=1)
topFrame.grid_columnconfigure(1, weight=1)
topFrame.grid_columnconfigure(2, weight=1)
middleFrame = LabelFrame(root, text="Input data")
middleFrame.grid(row=1, column=0, padx=8, pady=8, sticky=N+E+S+W)
middleFrame.grid_rowconfigure(0, weight=1)
middleFrame.grid_rowconfigure(1, weight=0)
middleFrame.grid_columnconfigure(0, weight=1)
middleFrame.grid_columnconfigure(1, weight=1)
bottomFrame = LabelFrame(root, text="Model Output")
bottomFrame.grid(row=2, column=0, padx=8, pady=8, sticky=N+E+S+W)
bottomFrame.grid_rowconfigure(0, weight=1)
bottomFrame.grid_columnconfigure(0, weight=1)
MyVar1 = IntVar()
MyVar2 = IntVar()
MyCheckbutton1 = Checkbutton(topFrame, text="x", variable=MyVar1)
MyCheckbutton1.grid(row=0, column=0, padx=4, pady=4)
Button1 = Button(topFrame, text="Choose xFile", command=forButton1)
Button1.grid(row=0, column=1, padx=4, pady=4)
Button3 = Button(topFrame, text="Clear")
Button3.grid(row=0, column=2, padx=4, pady=4)
MyCheckbutton2 = Checkbutton(topFrame, text="y", variable=MyVar2)
MyCheckbutton2.grid(row=1, column=0, padx=4, pady=4)
Button2 = Button(topFrame, text="Choose yFile", command=forButton2)
Button2.grid(row=1, column=1, padx=4, pady=4)
Button4 = Button(topFrame, text="Clear")
Button4.grid(row=1, column=2, padx=4, pady=4)
innerMiddleFrame = Frame(middleFrame)
innerMiddleFrame.grid(row=0, column=0, columnspan=2, padx=4, pady=4)
innerMiddleFrame.grid_columnconfigure(0, weight=1)
innerMiddleFrame.grid_columnconfigure(1, weight=0)
scrollbar = Scrollbar(innerMiddleFrame)
myList = Listbox(innerMiddleFrame, yscrollcommand=scrollbar.set)
myList.grid(row=0, column=0, sticky=N+E+S+W)
scrollbar.config(command=myList.yview)
scrollbar.grid(row=0, column=1, sticky=N+E+S+W)
Button5 = Button(middleFrame, text="Reset")
Button5.grid(row=1, column=0, padx=4, pady=4)
Button6 = Button(middleFrame, text="Submit")
Button6.grid(row=1, column=1, padx=4, pady=4)
Button7 = Button(bottomFrame, text="Exit", command=forButton7)
Button7.grid(row=0, column=0, padx=4, pady=4)
root.geometry("250x425")
root.mainloop()