Side by side output of SQL query (join three outputs)

You don't need to PIVOT, you need to JOIN[^] the tables; and I would also recommend that you use CTEs[^] to make it a little cleaner.

The CTE will basically encapsulate one of your queries into a one time use alias.
I would do this for each of your queries (different name for each one)

; WITH cteA AS (
	SELECT    BrCode, Code, Balance = sum((ClearBal+AccumuInt+clgamt)), Overdue = sum(OverdueAmt)
	FROM      LON20200331
	where     AcSts<>9
	AND       ClearBal<>0
	and       limit=1
	group by  BrCode,Code
		UNION ALL
	SELECT    BrCode, Code, Balance = sum((ClearBal+AccumuInt+clgamt)), Overdue = sum(OverdueAmt)
	FROM      ADV20200331 
	where     AcSts<>9 
	AND       ClearBal<0 
	and       limit=1 
	group by  BrCode,Code
)

Now should have 3 CTEs defined (I'll call them cteA, cteB, cteC), you can simply join them together.

SELECT a.Brcode, a.Code
,      BalanceL1 = a.Balance, OverdueL1 = a.Overdue
,      BalanceL2 = b.Balance, OverdueL2 = b.Overdue
,      BalanceL3 = c.Balance, OverdueL3 = c.Overdue

FROM       cteA
INNER JOIN cteB as b ON a.Brcode = b.BrCode AND a.Code = b.Code
INNER JOIN cteC as c ON a.Brcode = c.BrCode AND b.Code = c.Code

If you did all of this correctly... you should get zero results. That is because I used an INNER JOIN to tie these tables together; which will require that all 3 tables joined have the same [BrCode] and [code] values present.
The 3 CTEs were defined with a distinct value for Limit so the same brcode,code combination will not be in more than 1 table.

The solution is going to be another CTE to be JOINed in. This one will be just to get the codes, and will not need the aggregate values so there will be no GROUP BY. We only want each code combo once so the UNION will not contain ALL.

; WITH cteM as (
  SELECT Brcode,Code
  FROM   LON20200331 
  WHERE  AcSts<>9
  AND    ClearBal<>0
  AND    Limit IN (1, 2, 3)
      UNION
  SELECT BrCode,Code
  FROM   ADV20200331
  WHERE  AcSts<>9
  AND    ClearBal<0
  AND    Limit IN (1, 2, 3)
)

The JOIN method will be switched to aLEFT OUTER which will only require the value in the left half of the equation. The missing values to the right will be replaced with NULL

SELECT m.Brcode, m.Code
,      BalanceL1 = a.Balance, OverdueL1 = a.Overdue
,      BalanceL2 = b.Balance, OverdueL2 = b.Overdue
,      BalanceL3 = c.Balance, OverdueL3 = c.Overdue

FROM            cteM m
LEFT OUTER JOIN cteA a ON m.Brcode = a.BrCode AND m.Code = a.Code
LEFT OUTER JOIN cteB b ON m.Brcode = b.BrCode AND m.Code = b.Code
LEFT OUTER JOIN cteC c ON m.Brcode = c.BrCode AND m.Code = c.Code

This should get you a few results. You may need to do some work on your own, to get the results you want. I see potential flaws in this and I currently have my own work to do.

References:
Joins (SQL Server) - SQL Server | Microsoft Docs[^]
WITH common_table_expression (Transact-SQL) - SQL Server | Microsoft Docs[^]

Try this:

SELECT BrCode, Code, Balance1 = SUM(CASE WHEN [limit]=1 THEN BALANCE ELSE 0 END),
    Overdue1 = SUM(CASE WHEN [limit]=1 THEN Overdue ELSE 0 END),
    Balance2 = SUM(CASE WHEN [limit]=2 THEN BALANCE ELSE 0 END),
    Overdue2 = SUM(CASE WHEN [limit]=2 THEN BALANCE ELSE 0 END),
    Balance3 = SUM(CASE WHEN [limit]=3 THEN BALANCE ELSE 0 END),
    Overdue3 = SUM(CASE WHEN [limit]=3 THEN Overdue ELSE 0 END)
FROM
(
    SELECT BrCode, Code, SUM((ClearBal+AccumuInt+clgamt)) AS BALANCE,sum(OverdueAmt) Overdue, [limit]
    FROM LON20200331 
    WHERE AcSts<>9
    GROUP BY BrCode, Code, [limit]
    UNION ALL
    SELECT BrCode, Code, SUM((ClearBal+AccumuInt+clgamt)) AS BALANCE,sum(OverdueAmt) Overdue, [limit]
    FROM ADV20200331
    WHERE AcSts<>9
    GROUP BY BrCode, Code, [limit]
) T
GROUP BY BrCode, Code

or this:

SELECT BrCode, Code, pvt1.[1] AS Balance1, pvt2.[1] AS Overdue1,
    pvt1.[2] AS Balance2, pvt2.[2] AS Overdue2,
    pvt1.[3] AS Balance3, pvt2.[3] AS Overdue3 
FROM
(
    SELECT BrCode, Code, [1], [2], [3]
    FROM
    (
        SELECT BrCode, Code, [limit], SUM((ClearBal+AccumuInt+clgamt)) AS BALANCE
        FROM LON20200331  AS LON INNER JOIN ADV20200331 AS ADV ON LON.BrCode = ADV.BrCode AND LON.Code = ADV.Code
        WHERE AcSts<>9
        GROUP BY BrCode, Code, [limit]
    ) dt1
    PIVOT(SUM(BALANCE) FOR [limit] IN([1], [2], [3])) pt1
) pvt1 INNER JOIN 
(
    SELECT BrCode, Code, [1], [2], [3]
    FROM
    (
        SELECT BrCode, Code, [limit], SUM(OverdueAmt) AS Overdue
        FROM LON20200331  AS LON INNER JOIN ADV20200331 AS ADV ON LON.BrCode = ADV.BrCode AND LON.Code = ADV.Code
        WHERE AcSts<>9
        GROUP BY BrCode, Code, [limit]
    ) dt2
    PIVOT(SUM(Overdue) FOR [limit] IN([1], [2], [3])) pt2
) AS pvt2 ON pvt1.BarCode = pvt2.BarCode AND pvt1.Code = pvt2.Code